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iecat's Introduction

iECAT R-package

iECAT is an R-package for a method to integrating external controls in rare variant tests. It has functions for gene-based tests, including SKAT, and SKAT-O, and single variant test.

Link

Recommended Controls

  • Michigan Genomics Initiative Link
  • UK Biobank Link
  • NHLBI Exome Sequencing Project (ESP) Link

Reference

  • Lee, S., Kim, S., & Fuchsberger, C. (2017). Improving power for rare‐variant tests by integrating external controls. Genetic epidemiology, 41(7), 610-619.

iecat's People

Contributors

yatongli avatar leeshawn avatar

Stargazers

Ferdinando Bonfiglio avatar Fahri Küçükali avatar Sander W. van der Laan avatar

Watchers

Sander W. van der Laan avatar avatar

Forkers

seppinho yatongli kaskere

iecat's Issues

preparing controls

Hello,
I would like to run ieCAT, but is unclear, where to get GRCh38 exome external controls (.EC files), without liftover; With liftover there is risk to loose a lot of variants

Should I try to convert gnomAD v.3.1. genomes to exome control?

Thank you!

Error in rowSums(tbl.external.all) : 'x' must be numeric

Hello,
I try to run ieCAT, but have stopped into creating result file.

re<-iECAT.SSD.All(EC.INFO, obj=obj, method="optimal")
Error in rowSums(tbl.external.all) : 'x' must be numeric

fragments of my input files:
bim:

1       rs201219564     0       69270   A       G
1       rs2691305       0       69511   A       G
1       rs200505207     0       69761   A       T
1       rs200676709     0       69897   T       C

fam:

1       1        0 0 1 2
2       2        0 0 1 2
3       3        0 0 1 2

setID:

set1_183937        rs1169172101
set1_601436        rs373360530
set1_601667        rs879812396
set1_609407        rs61769279
set1_611317        rs12025928
set1_923421        rs7418179

EC

1       69183   rs1333310753    C       T       0       498
1       69200   rs1453226491    T       C       0       496
1       69208   rs1570409667    A       C       0       478
1       69335   rs773188222     G       A       0       1066
1       69404   rs1328728149    T       C       0       1486
1       69428   rs140739101     T       G       20      1652
1       69438   rs758790416     T       C       0       1768
1       69440   rs1424058787    T       G       0       1766
1       69448   rs1366217262    T       A       0       1828
1       69462   rs1217994907    C       G       0       1870

Here are the command lines I run:

library(SKAT)
library(MetaSKAT)
library(iECAT)
File.Bed<-"file.bed"
File.Bim<-"file.bim"
File.Fam<-"fam_all.fam"
File.SetID<-"file.setID"
File.EC<-("file.txt")
File.SSD<-"file.SSD"
File.Info<-"file.SSD.INFO"
File.EC.Info<-"file.SSD.ECINFO"
FAM<-Read_Plink_FAM(File.Fam, Is.binary=TRUE)
Generate_SSD_SetID_wEC(File.Bed, File.Bim, File.Fam, File.SetID, File.EC, File.SSD, File.Info, File.EC.Info)

EC.INFO= Open_SSD_wEC(File.SSD, File.Info, File.EC.Info)

obj<-SKAT_Null_Model(Phenotype ~ 1, out_type="D", data=FAM)
re<-iECAT.SSD.All(EC.INFO, obj=obj, method="optimal")
re

Is any additional argument needed in iECAT?

Update on iECAT_Main.R

Hi,

I appreciate your work on rare variant association tests integrating external controls. I used the iECAT_0.8.tar.gz released in 2017 and it works well on my data.

I read your recent paper "Novel score test to increase power in association test by integrating external controls" which using improved score tests by applying the Saddlepoint approximation and I also noticed "spa" appeared in your recent updated iECAT_Main.R. Could I ask that whether updated iECAT package is using the new score test that can do burden test and SKAT-O already?

Also, when I tried to install iECAT from GitHub that I met the problem that "525:55: unexpected numeric constant; 525: Z2 <- qnorm(min(p.value, p.value.tau1)2", is that possible it should be "qnorm(min(p.value, p.value.tau1)/2"?

Best wishes
YUE

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