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Check method argument in immune-deconv module #672

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Apr 4, 2020
Merged

Check method argument in immune-deconv module #672

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c57be2c
Sanity checking for method argument in immune deconv
Apr 3, 2020
6487811
Merge branch 'master' into method-deconv
jaclyn-taroni Apr 4, 2020
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8 changes: 6 additions & 2 deletions analyses/immune-deconv/01-immune-deconv.R
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Original file line number Diff line number Diff line change
Expand Up @@ -45,8 +45,12 @@ cibersort_bin <- opt$cibersortbin
cibersort_mat <- opt$cibersortgenemat
output.file <- opt$outputfile

print(cibersort_bin)
print(cibersort_mat)
#### Check model parameter - must be in deconvolution_methods (immunedeconv accepted options)
if (!(deconv.method %in% deconvolution_methods )){
stop( paste(c("Specified method not available. Must be one of the following: ", deconvolution_methods), collapse=" ") )
}


# if cibersort_bin and cibersort_mat are defined
# then, set path to cibersort binary and matrix
if(cibersort_bin != "NA" & cibersort_mat != "NA"){
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