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Fixes argument checking bug and data type bug #2

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Fixes argument checking bug and data type bug #2

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599a350
Fixes off-by-one error in argument checking
pirese Feb 20, 2020
2d727eb
Fixes study_map data type error in the case where input_type is equal…
pirese Feb 25, 2020
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7 changes: 4 additions & 3 deletions DISH/DISH.r
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Original file line number Diff line number Diff line change
Expand Up @@ -22,8 +22,8 @@ start = Sys.time()
print("reading arguments...")
args = commandArgs(TRUE)
argsLen <- length(args)
if (argsLen > 7) stop('error: You added too many arguments - usage: Rscript DISH.v2.r input_file MAF ethnicity(European/Asian) output')
if (argsLen < 6) stop('error: You need more auguments. check the usage - usage: Rscript DISH.v2.r input_file MAF ethnicity(European/Asian) output')
if (argsLen > 8) stop('error: You added too many arguments - usage: Rscript DISH.v2.r input_file input_type hg_version ethnicity MAF_threshold stat_type output (lambda)')
if (argsLen < 7) stop('error: You need more auguments. check the usage - usage: Rscript DISH.v2.r input_file input_type hg_version ethnicity MAF_threshold stat_type output (lambda)')

study_map_file = args[1]
if(!file.exists(study_map_file)){stop('error: The incorrect path of your input file')}
Expand Down Expand Up @@ -77,7 +77,8 @@ if(hg_ver == "hg18"){
## Check & Read the user defined input file
print("reading your input file...")
if(input_type=="T"){
study_map = complete.cases(read.table(study_map_file, header=T, sep="\t", stringsAsFactors=F))
data <- read.table(study_map_file, header=T, sep="\t", stringsAsFactors=F)
study_map <- data[complete.cases(data),]
}else if(input_type=="P"){
print("Merge your .frq file with your statistics information")
Ffile = read.table(pasete0(study_map_file,".frq",collapse=NULL), header=T,stringsAsFactors=F)
Expand Down