timflutre / eqtlbma Goto Github PK

Hi Tim,

I see that you have made some effort to make eqtlbma work on Mac OS X. I wanted to share with you my experiences installing eqtlbma on Mac OS X and perhaps we can provide some Mac-specific installation instructions for others on the Wiki.

I've found that Homebrew is key to making the installation process smoother, especially due to the constraints imposed by more recent editions of OS X (e.g., El Capitan). However, one should keep in mind that Homebrew seems to be in flux, so the exact steps may differ depending on the version of Homebrew used.

Here are the steps I took:

1. Install Homebrew 1.0.7 from http://brew.sh. Note before I need to install command-line tools: xcode-select --install. I'm using XCode 8.0.
2. Install gcc 4.8.5 using Homebrew: brew install homebrew/versions/gcc48
3. Install gsl 1.16: brew install homebrew/versions/gsl1
4. Install zlib 1.2.8: brew install homebrew/dupes/zlib
5. Install R 3.3.1 from http://r-project.org.
6. Install R package MASS 7.3-45.
7. Install eqtlbma 1.3.1:

./configure --prefix=/Users/msmith/eqtlbma \
  LDFLAGS="-L/usr/local/lib -L/usr/local/opt/zlib/lib" CXX="g++-4.8" \
  CPPFLAGS="-I/usr/local/include -I/usr/local/opt/zlib/include"

The only issue I've found so far is against with the tests. It is a strange problem in which zcmp does not work because sh does not seem to be supported. One solution is simply to use cmp instead of zcmp in the bash scripts. For example, in test_basic.bash, write

        gunzip obs_bf_sumstats_s${i}.txt.gz
        gunzip exp_bf_sumstats_s${i}.txt.gz
        if ! cmp -s obs_bf_sumstats_s${i}.txt exp_bf_sumstats_s${i}.txt; then
            echo "file 'obs_bf_sumstats_s${i}.txt.gz' has differences with exp"
            exit 1
        fi
        gzip obs_bf_sumstats_s${i}.txt
        gzip exp_bf_sumstats_s${i}.txt

Perhaps you can find a more elegant (or more compact) solution, but this works for me.

Peter

Hi,

I have a dataset of gene expression from 31 individuals measured in 4 conditions (A,B,C,D). I've installed the latest version of eqtlbma from the master branch and I've verified that /tests/test_basic.bash complete without errors. I've also beeb able to successfully complete the tutorial on simulated data without any problems.

However, when I'm trying to run it on my own data it works well for some genes, but for others I get segmentation faults that sometimes randomly disappear. For example the following command produces segmation fault > 90% of the time:

eqtlbma_bf --geno eqtlbma/list_genotypes.txt
--scoord eqtlbma/snp_coords.bed.gz
--exp eqtlbma/list_explevels_HLA.txt
--gcoord eqtlbma/HLA_coord.txt
--anchor TSS
--cis 500000
--out eqtlbma/output/subset_test
--analys join --gridL eqtlbma/grid_phi2_oma2_general.txt
--gridS eqtlbma/grid_phi2_oma2_with-configs.txt
--bfs all
--error mvlr
-v 3

test for association between each pair gene-SNP ...
analysis=join likelihood=normal error_model=mvlr prop_cov_errors=0.50 anchor=TSS radius=500000
gene ENSG00000196735
339 cis SNP(s)
ENSG00000196735 (4 subgroups) versus exm-rs3830076 (4 subgroups)
ENSG00000196735 (4 subgroups) versus exm534565 (4 subgroups)
ENSG00000196735 (4 subgroups) versus rs4713505;exm-rs4713505 (4 subgroups)
ENSG00000196735 (4 subgroups) versus exm-rs204999 (4 subgroups)
ENSG00000196735 (4 subgroups) versus exm-rs3130279 (4 subgroups)
ENSG00000196735 (4 subgroups) versus exm-rs4713506 (4 subgroups)
...
ENSG00000196735 (4 subgroups) versus exm-rs2395110 (4 subgroups)
ENSG00000196735 (4 subgroups) versus exm-rs6936204 (4 subgroups)
ENSG00000196735 (4 subgroups) versus exm-rs3115573 (4 subgroups)
Segmentation fault

I'm happy to send you the example data for you to replicate the issue.

Best wishes,
Kaur

This is what I get. Is there something I miss?
Same in Mac and on Centos 7

user@server { /biosoftware/eqtlbma }$ autoconf
configure.ac:5: error: possibly undefined macro: AM_INIT_AUTOMAKE
      If this token and others are legitimate, please use m4_pattern_allow.
      See the Autoconf documentation.
configure.ac:8: error: possibly undefined macro: AM_PROG_AR
configure.ac:21: error: possibly undefined macro: AM_SILENT_RULES
user@server  { /biosoftware/eqtlbma }$ ./configure
configure: error: cannot find install-sh, install.sh, or shtool in build-aux "."/build-aux
user@server { /biosoftware/eqtlbma }$

We had an issue where the program would terminate abnormally, and it looks like the culprit was snprintf() in the function getDateTime(). The char buffer is 100 bytes, but snprintf attempts to write 126. The compiler also gives a warning about it that I didn't notice originally:

In function ‘int snprintf(char*, size_t, const char*, ...)’,
inlined from ‘std::string getDateTime(const time_t&)’ at utils.cpp:172:48:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:66:44: warning: call to int __builtin___snprintf_chk(char*, long unsigned int, int, long unsigned int, const char*, ...) will always overflow destination

Changing char buffer[100] to char buffer[126] within that function solved the problem for us.

Hi Tim,

I'm using eqtlbma 1.3.1. I successfully ran ./configure and make (on a compute cluster with Scientific Linux 6). However, when I ran make test, this is the output I got (in test-suite.log):

   eqtlbma 1.3.1: tests/test-suite.log
=========================================

# TOTAL: 11
# PASS:  10
# SKIP:  0
# XFAIL: 0
# FAIL:  1
# XPASS: 0
# ERROR: 0

.. contents:: :depth: 2

FAIL: test_common-uniq-inds.bash
================================

START test_common-uniq-inds.bash 2016-10-10 17:38:26
cmd-line: ./test_common-uniq-inds.bash
temp dir: /project/mstephens/eqtlbma-1.3.1/tests/tmp_test_30612
simulate data and calculate expected results ...
analyze data to get observed results ...
compare obs vs exp results ...

Further:

> cat test_common-uniq-inds.bash.log
START test_common-uniq-inds.bash 2016-10-10 17:38:26
cmd-line: ./test_common-uniq-inds.bash
temp dir: /project/mstephens/eqtlbma-1.3.1/tests/tmp_test_30612
simulate data and calculate expected results ...
analyze data to get observed results ...
compare obs vs exp results ...
file 'obs_bf_l10abfs_raw.txt.gz' has differences with exp

A quick scan of the two files, exp_bf_l10abfs_raw.txt.gz and obs_bf_l10abfs_raw.txt.gz, and the results are clearly not even close. I've attached the files from the test foilder so you can look at them yourself.

Any idea what might be the problem? Perhaps it has something to do with the simulated data being different (e.g., because the sequence of pseudorandom numbers is different)?

Thanks,
Peter

tmp_test_30612.tar.gz

Hello,

When I run the package it produces the error below:
"configure: error: unable to find the gslcblas library with the cblas_sgemm() function"
Is it due to the gsl not being linked?

ps:the sever has the gsl installed.
Thanks!
Ming

Hi,
When I use eqtlbma_bf, I found that it loaded keep no SNP from vcf file. My vcf file didn't contatin any SNPs with missing genotypes because I already filtered before. So I wonder what caused this.
Here is my commond and outputs of eqtlbam_bf.

eqtlbma_bf --geno list_genotypes.txt --exp list_explevels.txt --gcoord gene_coords.bed.gz --anchor TSS --cis 1000000 --out out_eqtlbma --analys join --covar list_covariates.txt --gridL grid_phi2_oma2_general.txt --gridS grid_phi2_oma2_with-configs.txt --bfs all --error mvlr --thread=4

load file list_explevels.txt ...
items loaded: 2
load file list_genotypes.txt ...
items loaded: 2
load file list_covariates.txt ...
items loaded: 2
analyze 2 subgroups (identifier):
Normal (1)
Tumor (2)
load samples ...
nb of samples (explevels): 268
Normal: 134 samples
Tumor: 134 samples
nb of samples (genotypes): 134
Normal: 134 samples
Tumor: 134 samples
total nb of samples: 268
nb of samples (covariates): 134
Normal: 134 samples
Tumor: 134 samples
load covariates ...
Normal (/data/wjxu/HRA000099/MatrixEQTL/3_eqtlbma/eQTL/Covariates_normal.txt.gz): 21 covariates
Tumor (/data/wjxu/HRA000099/MatrixEQTL/3_eqtlbma/eQTL/Covariates_tumor.txt.gz): 22 covariates
load gene coordinates ...
total nb of genes with coordinates: 35252
load gene expression levels ...
Normal (/data/wjxu/HRA000099/MatrixEQTL/3_eqtlbma/eQTL/Expression_normalization_normal.txt.gz): 35252 genes (to keep: 35252)
Tumor (/data/wjxu/HRA000099/MatrixEQTL/3_eqtlbma/eQTL/Expression_normalization_tumor.txt.gz): 35252 genes (to keep: 35252)
total nb of genes to analyze: 35252
load genotypes and SNP coordinates ...
Normal (/data/wjxu/HRA000099/MatrixEQTL/3_eqtlbma/eQTL/combined.134.nomiss.recode.vcf.gz): 5444712 SNPs (to keep: 0, loaded in 111.38 sec)
discard SNPs with missing values ...
duplicate genotypes for other subgroups (same file) ...
Tumor (/data/wjxu/HRA000099/MatrixEQTL/3_eqtlbma/eQTL/combined.134.nomiss.recode.vcf.gz): 0 SNPs duplicated in 0.00 sec
nb of SNPs: 0
END lt-eqtlbma_bf 2023-03-16 21:11:55
elapsed -> 0d 0h 1m 59s
max.mem -> 100732 kB

Hi,

I am writing because I am not able to install the eqtlbma software.

After downloading it, I attempted to convert the configure.ac file to configure using autoconf, but I get the following error:

configure.ac:8: error: possibly undefined macro: AM_INIT_AUTOMAKE
If this token and others are legitimate, please use m4_pattern_allow.
See the Autoconf documentation.
configure.ac:11: error: possibly undefined macro: AM_PROG_AR
configure.ac:24: error: possibly undefined macro: AM_SILENT_RULES

Any help/suggestion would be greatly appreciated.

Thanks,
Oana

Hi,

Thank you very much for all your help.

I have some additional questions, after having run this program.

1. when I specify the error term as mvlr, I always get an error saying matrix is singular. I tried changing the error term to uvlr, and that solves the problem. However, I believe I really should be using the mvlr, because in all my tissues I have the exact same individuals.

Run (I shortened filenames for clarity):
cmd-line: lt-eqtlbma_bf --geno _geno_chr21 --exp exp_chr21 --scoord 21_snppos.bed.gz --gcoord expTSS.bed --anchor TSS --cis 1000000 --out chr21 --type join --gridL grid_phi2_oma2_general.txt.gz --gridS grid_phi2_oma2_with-configs.txt.gz --bfs all --error mvlr --qnorm

Error reproduced here:
total nb of SNPs to analyze: 122816
load grid in /srv/gs1/projects/snyder/jzaugg/histoneQTL/jointQTL/data/grid_phi2_oma2_general.txt.gz ...
grid size: 25
load grid in /srv/gs1/projects/snyder/jzaugg/histoneQTL/jointQTL/data/grid_phi2_oma2_with-configs.txt.gz ...
grid size: 10
look for association between each pair gene-SNP ...
likelihood=normal errors=mvlr prop_cov_errors=0.50 anchor=TSS radius=1000000
=========================================== 86.22%gsl: lu.c:262: ERROR: matrix is singular
Default GSL error handler invoked.
Aborted

2. when I run eqtlbma_bf, i get nan for some values on the grid, and some rows. Is that normal, or does that indicate an error?

Run: same as above but with uvlr

Here is an example:
gene snp config l10abf.grid1 l10abf.grid2 l10abf.grid3 l10abf.grid4 l10abf.grid5 l10abf.grid6 l10abf.grid7 l10abf.grid8 l10abf.grid9 l10abf.grid10 l10abf.grid11 l10abf.grid12 l10abf.grid13 l10abf.grid14 l10abf.grid15 l10abf.grid16 l10abf.grid17 l10abf.grid18 l10abf.grid19 l10abf.grid20 l10abf.grid21 l10abf.grid22 l10abf.grid23 l10abf.grid24 l10abf.grid25
g1 rs74700993 gen 3.010325e-02 6.667264e-02 1.008149e-01 1.328496e-01 1.630494e-01 7.337196e-02 1.597779e-01 2.327912e-01 2.974713e-01 3.572021e-01 1.822143e-02 1.187750e-01 2.098473e-01 3.090112e-01 4.317469e-01 -3.918792e-01 -3.247306e-01 -2.239222e-01-5.721876e-02 2.875899e-01 -1.117384e+00 -1.071324e+00 -9.621280e-01 -7.397135e-01 3.290463e-02
g1 rs74700993 gen-fix 1.630494e-01 1.630494e-01 1.630494e-01 1.630494e-01 1.630494e-01 3.572021e-01 3.572021e-01 3.572021e-01 3.572021e-01 3.572021e-01 4.317469e-01 4.317469e-01 4.317469e-01 4.317469e-01 4.317469e-01 2.875899e-01 2.875899e-01 2.875899e-01 2.875899e-01 2.875899e-01 3.290463e-02 3.290463e-02 3.290463e-02 3.290463e-02 3.290463e-02
g1 rs74700993 gen-maxh 3.010325e-02 3.010325e-02 3.010325e-02 3.010325e-02 3.010325e-02 7.337196e-02 7.337196e-02 7.337196e-02 7.337196e-02 7.337196e-02 1.822143e-02 1.822143e-02 1.822143e-02 1.822143e-02 1.822143e-02 -3.918792e-01 -3.918792e-01 -3.918792e-01 -3.918792e-01 -3.918792e-01 -1.117384e+00 -1.117384e+00 -1.117384e+00 -1.117384e+00 -1.117384e+00
g1 rs74700993 1 2.033034e-02 2.033034e-02 5.713568e-02 5.713568e-02 7.765497e-02 7.765497e-02 -2.871425e-02-2.871425e-02 -2.584742e-01 -2.584742e-01 nan nan nan nan nan nan nan nan nan nan nan nan nan nan nan
g1 rs74700993 2 -6.194595e-03 -6.194595e-03 -2.705216e-02 -2.705216e-02 -1.067565e-01 -1.067565e-01 -2.912661e-01-2.912661e-01 -5.521341e-01 -5.521341e-01 nan nan nan nan nan nan nan nan nan nan nan nan nan nan nan
g1 rs74700993 3 1.596751e-02 1.596751e-02 4.328844e-02 4.328844e-02 4.732293e-02 4.732293e-02 -7.189885e-02-7.189885e-02 -3.067755e-01 -3.067755e-01 nan nan nan nan nan nan nan nan nan nan nan nan nan nan nan
g1 rs74700993 1-2 4.465814e-02 5.430667e-02 1.034399e-01 1.262786e-01 7.861843e-02 1.307712e-01 -1.820693e-01-2.673854e-02 -6.462906e-01 -2.828212e-01 nan nan nan nan nan nan nan nan nan nan nan nan nan nan nan
g1 rs74700993 1-3 8.582202e-02 1.014462e-01 2.179070e-01 2.537697e-01 2.822355e-01 3.529339e-01 6.380535e-02 2.460691e-01 -3.920003e-01 6.473547e-03 nan nan nan nan nan nan nan nan nan nan nan nan nan nan nan
g1 rs74700993 2-3 3.869692e-02 4.789267e-02 8.651767e-02 1.089317e-01 4.663703e-02 1.005428e-01 -2.248914e-01-6.385790e-02 -6.942270e-01 -3.221839e-01 nan nan nan nan nan nan nan nan nan nan nan nan nan nan nan

Thank you very much,
Oana

Hi,
Using eqtlbma-1.2.2, I first run eqtlbma with the parameters corresponding to BF_{BMA}, that is, "--bfs all --pbf all" with 4 subgroups and everything seems to run smoothly and all BFs are reported for all snp-gene pairs. However, when I run hm like this:

/launch_hm.bash
--p2b /path/to/hm
--inp /path/to/"eqtlbma_out.bfbma.gene100*_l10abfs_raw.txt.gz"
--nbC 15
--nbG 10
--skip-ci
--outp /path/to/eqtlbma_hm_out_test &

The stderr reports 'nan' for all parameters and all iterations and runs, seemingly, ad infinitum. There are indeed 15 active configurations (i.e. 4 subgroups) and 10 grid points (in --gridS) and the temporary input_hm_XXXXX.txt file shows reasonable BFs for all configs by grid points. I feel like I may be missing something simple here, any recommendations?

Thanks so much,
Ian

compute quasi poisson likelihood using eqtlbma parallel

Hi,
When I run eqtlbma_hm, I got this error. I wonder what caused this. Is this due to nan being included in the output of the eqtlbma_bf?
Here is commond and error.

zless out_eqtlbma_l10abfs_raw.txt.gz |head
gene    snp     config  l10abf.grid1    l10abf.grid2    l10abf.grid3    l10abf.grid4    l10abf.grid5    l10abf.grid6    l10abf.grid7    l10abf.grid8    l10abf.grid9    l10abf.grid10   l10abf.grid11  l10abf.grid12    l10abf.grid13   l10abf.grid14   l10abf.grid15   l10abf.grid16   l10abf.grid17   l10abf.grid18   l10abf.grid19   l10abf.grid20   l10abf.grid21   l10abf.grid22   l10abf.grid23   l10abf.grid24   l10abf.grid25
7SK     chr1_119228079_G_A      gen     -2.552074e-01   -2.567767e-01   -2.533767e-01   -2.456162e-01   -2.354144e-01   -6.356711e-01   -6.296440e-01   -6.055082e-01   -5.571040e-01   -4.747932e-01  -1.160806e+00    -1.149360e+00   -1.109070e+00   -1.018222e+00   -7.573831e-01   -1.741525e+00   -1.728199e+00   -1.681967e+00   -1.572422e+00   -1.053561e+00   -2.338098e+00   -2.324259e+00   -2.276372e+00   -2.161275e+00   -1.353362e+00
7SK     chr1_119228079_G_A      gen-fix -2.354144e-01   -2.354144e-01   -2.354144e-01   -2.354144e-01   -2.354144e-01   -4.747932e-01   -4.747932e-01   -4.747932e-01   -4.747932e-01   -4.747932e-01  -7.573831e-01    -7.573831e-01   -7.573831e-01   -7.573831e-01   -7.573831e-01   -1.053561e+00   -1.053561e+00   -1.053561e+00   -1.053561e+00   -1.053561e+00   -1.353362e+00   -1.353362e+00   -1.353362e+00   -1.353362e+00   -1.353362e+00
7SK     chr1_119228079_G_A      gen-maxh        -2.552074e-01   -2.552074e-01   -2.552074e-01   -2.552074e-01   -2.552074e-01   -6.356711e-01   -6.356711e-01   -6.356711e-01   -6.356711e-01   -6.356711e-01   -1.160806e+00   -1.160806e+00   -1.160806e+00   -1.160806e+00   -1.160806e+00   -1.741525e+00   -1.741525e+00   -1.741525e+00   -1.741525e+00   -1.741525e+00   -2.338098e+00   -2.338098e+00  -2.338098e+00    -2.338098e+00   -2.338098e+00
7SK     chr1_119228079_G_A      1       -1.811154e-01   -1.811154e-01   -3.965886e-01   -3.965886e-01   -6.696843e-01   -6.696843e-01   -9.631312e-01   -9.631312e-01   -1.262223e+00   -1.262223e+00  nan      nan     nan     nan     nan     nan     nan     nan     nan     nan     nan     nan     nan     nan     nan
7SK     chr1_119228079_G_A      2       -7.409202e-02   -7.409202e-02   -2.390825e-01   -2.390825e-01   -4.911213e-01   -4.911213e-01   -7.783937e-01   -7.783937e-01   -1.075875e+00   -1.075875e+00  nan      nan     nan     nan     nan     nan     nan     nan     nan     nan     nan     nan     nan     nan     nan
7SK     chr1_119228079_G_A      1-2     -2.456162e-01   -2.354144e-01   -5.571040e-01   -4.747932e-01   -1.018222e+00   -7.573831e-01   -1.572422e+00   -1.053561e+00   -2.161275e+00   -1.353362e+00  nan      nan     nan     nan     nan     nan     nan     nan     nan     nan     nan     nan     nan     nan     nan
7SK     chr1_119230040_T_C      gen     -1.723150e-01   -1.643266e-01   -1.528507e-01   -1.376136e-01   -1.194407e-01   -5.136785e-01   -5.026857e-01   -4.744328e-01   -4.214989e-01   -3.291333e-01  -1.022504e+00    -1.009488e+00   -9.678831e-01   -8.753246e-01   -6.017647e-01   -1.598441e+00   -1.584697e+00   -1.538113e+00   -1.428078e+00   -8.952365e-01   -2.193767e+00   -2.179821e+00   -2.131845e+00   -2.016620e+00   -1.194346e+00
7SK     chr1_119230040_T_C      gen-fix -1.194407e-01   -1.194407e-01   -1.194407e-01   -1.194407e-01   -1.194407e-01   -3.291333e-01   -3.291333e-01   -3.291333e-01   -3.291333e-01   -3.291333e-01  -6.017647e-01    -6.017647e-01   -6.017647e-01   -6.017647e-01   -6.017647e-01   -8.952365e-01   -8.952365e-01   -8.952365e-01   -8.952365e-01   -8.952365e-01   -1.194346e+00   -1.194346e+00   -1.194346e+00   -1.194346e+00   -1.194346e+00
7SK     chr1_119230040_T_C      gen-maxh        -1.723150e-01   -1.723150e-01   -1.723150e-01   -1.723150e-01   -1.723150e-01   -5.136785e-01   -5.136785e-01   -5.136785e-01   -5.136785e-01   -5.136785e-01   -1.022504e+00   -1.022504e+00   -1.022504e+00   -1.022504e+00   -1.022504e+00   -1.598441e+00   -1.598441e+00   -1.598441e+00   -1.598441e+00   -1.598441e+00   -2.193767e+00   -2.193767e+00  -2.193767e+00    -2.193767e+00   -2.193767e+00

cmd-line: /data/wjxu/software/eqtlbma-1.3.3/src/.libs/lt-eqtlbma_hm --data out_eqtlbma_l10abfs.txt.gz --nsubgrp 3 --dim 7 --ngrid 10 --out test_eqtlbma_hm.txt.gz
load data ...
nb of input files: 1
==================================================100.00%
finish loading 35252 genes and 174735745 gene-snp pairs (4065.900000 sec, 678283676 kB)
run EM algorithm (classic) ...
iter    0  loglik 18710.126792  pi0 5.0000e-01  configs 1.4286e-01 1.4286e-01 1.4286e-01 1.4286e-01 1.4286e-01 1.4286e-01 1.4286e-01  grid-points 1.0000e-01 1.0000e-01 1.0000e-01 1.0000e-01 1.0000e-01 1.0000e-01 1.0000e-01 1.0000e-01 1.0000e-01 1.0000e-01
ERROR: new_config_prior_[3] is NaN
terminate called after throwing an instance of 'int'

Hi,

Thank you very much for all your help.

I have some additional questions, after having run this program.

1) when I specify the error term as mvlr, I always get an error saying matrix is singular. I tried changing the error term to uvlr, and that solves the problem. However, I believe I really should be using the mvlr, because in all my tissues I have the exact same individuals.

Run (I shortened filenames for clarity):
cmd-line: lt-eqtlbma_bf --geno _geno_chr21 --exp exp_chr21 --scoord 21_snppos.bed.gz --gcoord expTSS.bed --anchor TSS --cis 1000000 --out chr21 --type join --gridL grid_phi2_oma2_general.txt.gz --gridS grid_phi2_oma2_with-configs.txt.gz --bfs all --error mvlr --qnorm

Error reproduced here:
total nb of SNPs to analyze: 122816
load grid in /srv/gs1/projects/snyder/jzaugg/histoneQTL/jointQTL/data/grid_phi2_oma2_general.txt.gz ...
grid size: 25
load grid in /srv/gs1/projects/snyder/jzaugg/histoneQTL/jointQTL/data/grid_phi2_oma2_with-configs.txt.gz ...
grid size: 10
look for association between each pair gene-SNP ...
likelihood=normal errors=mvlr prop_cov_errors=0.50 anchor=TSS radius=1000000
=========================================== 86.22%gsl: lu.c:262: ERROR: matrix is singular
Default GSL error handler invoked.
Aborted

2) when I run eqtlbma_bf, i get nan for some values on the grid, and some rows. Is that normal, or does that indicate an error?

Run: same as above but with uvlr

Here is an example:
gene snp config l10abf.grid1 l10abf.grid2 l10abf.grid3 l10abf.grid4 l10abf.grid5 l10abf.grid6 l10abf.grid7 l10abf.grid8 l10abf.grid9 l10abf.grid10 l10abf.grid11 l10abf.grid12 l10abf.grid13 l10abf.grid14 l10abf.grid15 l10abf.grid16 l10abf.grid17 l10abf.grid18 l10abf.grid19 l10abf.grid20 l10abf.grid21 l10abf.grid22 l10abf.grid23 l10abf.grid24 l10abf.grid25
g1 rs74700993 gen 3.010325e-02 6.667264e-02 1.008149e-01 1.328496e-01 1.630494e-01 7.337196e-02 1.597779e-01 2.327912e-01 2.974713e-01 3.572021e-01 1.822143e-02 1.187750e-01 2.098473e-01 3.090112e-01 4.317469e-01 -3.918792e-01 -3.247306e-01 -2.239222e-01-5.721876e-02 2.875899e-01 -1.117384e+00 -1.071324e+00 -9.621280e-01 -7.397135e-01 3.290463e-02
g1 rs74700993 gen-fix 1.630494e-01 1.630494e-01 1.630494e-01 1.630494e-01 1.630494e-01 3.572021e-01 3.572021e-01 3.572021e-01 3.572021e-01 3.572021e-01 4.317469e-01 4.317469e-01 4.317469e-01 4.317469e-01 4.317469e-01 2.875899e-01 2.875899e-01 2.875899e-01 2.875899e-01 2.875899e-01 3.290463e-02 3.290463e-02 3.290463e-02 3.290463e-02 3.290463e-02
g1 rs74700993 gen-maxh 3.010325e-02 3.010325e-02 3.010325e-02 3.010325e-02 3.010325e-02 7.337196e-02 7.337196e-02 7.337196e-02 7.337196e-02 7.337196e-02 1.822143e-02 1.822143e-02 1.822143e-02 1.822143e-02 1.822143e-02 -3.918792e-01 -3.918792e-01 -3.918792e-01 -3.918792e-01 -3.918792e-01 -1.117384e+00 -1.117384e+00 -1.117384e+00 -1.117384e+00 -1.117384e+00
g1 rs74700993 1 2.033034e-02 2.033034e-02 5.713568e-02 5.713568e-02 7.765497e-02 7.765497e-02 -2.871425e-02-2.871425e-02 -2.584742e-01 -2.584742e-01 nan nan nan nan nan nan nan nan nan nan nan nan nan nan nan
g1 rs74700993 2 -6.194595e-03 -6.194595e-03 -2.705216e-02 -2.705216e-02 -1.067565e-01 -1.067565e-01 -2.912661e-01-2.912661e-01 -5.521341e-01 -5.521341e-01 nan nan nan nan nan nan nan nan nan nan nan nan nan nan nan
g1 rs74700993 3 1.596751e-02 1.596751e-02 4.328844e-02 4.328844e-02 4.732293e-02 4.732293e-02 -7.189885e-02-7.189885e-02 -3.067755e-01 -3.067755e-01 nan nan nan nan nan nan nan nan nan nan nan nan nan nan nan
g1 rs74700993 1-2 4.465814e-02 5.430667e-02 1.034399e-01 1.262786e-01 7.861843e-02 1.307712e-01 -1.820693e-01-2.673854e-02 -6.462906e-01 -2.828212e-01 nan nan nan nan nan nan nan nan nan nan nan nan nan nan nan
g1 rs74700993 1-3 8.582202e-02 1.014462e-01 2.179070e-01 2.537697e-01 2.822355e-01 3.529339e-01 6.380535e-02 2.460691e-01 -3.920003e-01 6.473547e-03 nan nan nan nan nan nan nan nan nan nan nan nan nan nan nan
g1 rs74700993 2-3 3.869692e-02 4.789267e-02 8.651767e-02 1.089317e-01 4.663703e-02 1.005428e-01 -2.248914e-01-6.385790e-02 -6.942270e-01 -3.221839e-01 nan nan nan nan nan nan nan nan nan nan nan nan nan nan nan

Thank you very much,
Oana

Hi,

I am posting this question here because I am having trouble viewing/accessing the mailing list.

In the bayes factor file outputted by eqtlbma_bf (or indeed any reference to a configuration), is there a record of which subgroup each number in the various configuration strings corresponds to? I.e. if i have 4 subgroups, "Skin", "Heart", "Liver", and "Lung", a configuration of 1-3 corresponds to activity in which two tissues? looking at a few examples, it doesn't seem to be based on the order in which subgroup files are listed in --exp or --inss, but maybe I'm missing something obvious.

Thanks,
Sahin

I am trying to rebuild the package with GSL 2.1 and I am getting the following errors:

Making all in src/eqtlbma
make[1]: Entering directory '/home/dacre/my_packages/eqtlbma/eqtlbma/src/eqtlbma-1.3.1/src/eqtlbma'
Making all in utils
make[2]: Entering directory '/home/dacre/my_packages/eqtlbma/eqtlbma/src/eqtlbma-1.3.1/src/eqtlbma/utils'
  CXX      utils_math.lo
utils_math.cpp: In function ‘void utils::FitSingleGeneWithSingleSnp(const gsl_matrix*, const gsl_vector*, double&, double&, double&, double&, double&)’:
utils_math.cpp:185:72: error: cannot convert ‘const gsl_vector*’ to ‘gsl_multifit_linear_workspace*’ for argument ‘2’ to ‘int gsl_multifit_linear_svd(const gsl_matrix*, gsl_multifit_linear_workspace*)’
                                              Bhat, covBhat, &rss, work);
                                                                        ^
make[2]: *** [Makefile:373: utils_math.lo] Error 1
make[2]: Leaving directory '/home/dacre/my_packages/eqtlbma/eqtlbma/src/eqtlbma-1.3.1/src/eqtlbma/utils'
make[1]: *** [Makefile:535: all-recursive] Error 1
make[1]: Leaving directory '/home/dacre/my_packages/eqtlbma/eqtlbma/src/eqtlbma-1.3.1/src/eqtlbma'
make: *** [Makefile:391: all-recursive] Error 1

Is this something you have noticed or is this a bug on my end? I am just doing a simple configure, make combo the same way I always used to using version 1.3.1, but it is failing. Any thoughts?

A useful enhancement would be the option to defining cis in respect to TSS and TES.

Hello,
I'm trying to install the latest version (v1.3) and I see that there is no configure file in either the git repo or the zip file of the master branch.

I did the following:
$ git clone https://github.com/timflutre/eqtlbma.git
$ find eqtlbma/ -type f -iname "configure"
eqtlbma/configure.ac

And :
$ cd eqtlbma/
$ make
make: *** No targets specified and no makefile found. Stop.

Any help would be appreciated.

Thanks,
Anand

Hi,

Thank you very much for all your help and responses.
As I was going through your method explained in the paper, I want to ask about how you choose the significant QTLs.

To my understanding, for the comparison between eqtlbma and the tissue-by-tissue analysis, you perform permutations, and then get pvalues for each gene based on the empirical distribution of the test statistic (min pvalue for the tissue-by-tissue analysis and the average BF for the jointQTL analysis). However, one gets these permutation results after just running eqtlbma_bf, and I believed that the test statistic for the jointQTL analysis would be the BF you get at the end, when BFs from each configuration are weighted accordingly.

Would it be possible to clarify how the Bayesian Model Averaging is used for deciding significant QTLs at a given FDR?

Thank you,
Oana

Hi,

I just cloned eqtlbma from github today, and ran the test_basic.bash
I got an error saying segmentation fault (below), and I wanted to check whether you have any advice on how to solve this. I made no modification at all in the test files.

Thank you,
Oana

Error below:
/home/oursu/devtools/eqtlbma3/eqtlbma/tests/test_basic.bash --p2e /home/oursu/devtools/eqtlbma3/eqtlbma/src/eqtlbma_bf --p2R /home/oursu/devtools/eqtlbma3/eqtlbma/tests/functional_tests.R
START test_basic.bash 2014-04-26 22:52:05
cmd-line: /home/oursu/devtools/eqtlbma3/eqtlbma/tests/test_basic.bash --p2e /home/oursu/devtools/eqtlbma3/eqtlbma/src/eqtlbma_bf --p2R /home/oursu/devtools/eqtlbma3/eqtlbma/tests/functional_tests.R
temp dir: /home/oursu/tmp_test_16332
simulate data and calculate expected results ...
analyze data to get observed results ...
/home/oursu/devtools/eqtlbma3/eqtlbma/tests/test_basic.bash: line 108: 16354 Segmentation fault (core dumped) $pathToBf --geno list_genotypes.txt --scoord snp_coords.bed.gz --exp list_phenotypes.txt --gcoord gene_coords.bed.gz --cis 5 --out obs_bf --outss --outw --type join --bfs all --gridL grid_phi2_oma2_general.txt.gz --gridS grid_phi2_oma2_with-configs.txt.gz -v 1 &>stdout_bf
compare obs vs exp results ...
/usr/bin/zdiff: line 68: obs_bf_sumstats_s1.txt.gz: No such file or directory
file 'obs_bf_sumstats_s1.txt.gz' has differences with exp

Following up on my comments in #22, the release 1.3.2 also fails to compile under GSL 2.1 (the API change referred to in #22 changed in 2.0 (see here). A new release would help us update the bioconda package ASAP.