When executing the command:

install_github("transbioZI/Gimpute", build_vignettes=TRUE)

I get this error:

Error: Failed to install 'Gimpute' from GitHub:
System command 'Rcmd.exe' failed, exit status: 1, stdout + stderr (last 10 lines):
E> --- re-building 'GimputeTutorial.Rmd' using rmarkdown
E> Error: processing vignette 'GimputeTutorial.Rmd' failed with diagnostics:
E> The 'rmarkdown' package should be installed and declared as a dependency of the 'Gimpute' package (e.g., in the 'Suggests' field of DESCRIPTION), because the latter contains vignette(s) built with the 'rmarkdown' package. Please see yihui/knitr#1864 for more information.

Would it be possible to fix this error?

The file R/phasingImpute4.R has the comment

## impute for chrX PAR >> with an additional flag: --Xpar.

However, the lines following it and running IMPUTE4 do not have that flag set, i.e.

167:                ## impute for chrX PAR >> with an additional flag: --Xpar.
168-                system(paste0(impute4,   
169-                " -no_maf_align \ ",   
170-                " -m ", GENMAP_FILE, " \ ",  
171-                " -h ", HAPS.chrXPAR1, " \ ", 
172-                " -l ", LEGEND.chrXPAR1, " \ ", 
173-                " -g ", GWAS_HAPS_FILE, " \ ", 
174-                " -Ne ", effectiveSize, " \ ", 
175-                " -int ", chunkSTART, " ", chunkEND, " \ ", 
176-                " -buffer 1000  \ ",
177-                " -o ", OUTPUT_FILE, " \ " ))
178-            } else if (i == "X_PAR2") {  

Could you please clarify whether the effectiveSize is being reduced elsewhere in order to mimic the effect of the missing flag as per IMPUTE2?
Thanks

Hi,

Thank you for developing Gimpute. I looking forward to use you pipeline for imputation and have some questions I hope you can help me with.

I have data from PsycArray_B (37) and read in your instruktions that there are two types of geneotyping chip annotation file: "SNP_" and "rs" . PsychChip_B is a mix of SNP_ and rs-numbers.

So my qustion is: is the rs-number used in the imputation or is it enough with position and strand? If the rs-number is used, are the non-rs probes exluded and should I translate as many as possible probeIDs to rs-number and rename the probe IDs?

Cheers,
Christian

Hi,
In genotypeInfoUpdate.R.

line 920 - 924.

step 3 replace group IDs

metaDataFile <- "1_01_metaData.txt" 
outputPrefix3 <- "1_03_replacedGroupAndSex"
updateGroupIdAndSex(plink, inputPrefix=outputPrefix2, 
                    metaDataFile, outputPrefix=outputPrefix3)

The "metaDataFile <- "1_01_metaData.txt"" is overwriting the naming of the metaData file, so we are forced to name the metadata file "1_01_metaData.txt".

It would be nice if you could remove the line, so we can name the metadata file!

Cheers,
Christian