Open mocksu opened 1 year ago
My data file looks like this:
SNPID BETA SE A1 A2 Phenotype F CHR POS N PVAL NOTE ProbeID rs6883726 0.00191 0.05288 T C GENE123 0.4014557849133537 5 157750134 750 0.97115 N/A PS123 rs6864758 0.00185 0.05288 G A GENE123 0.3983578618756371 5 157750349 750 0.97209 N/A PS123 rs6883448 0.00179 0.05287 C T GENE123 0.4014318934760449 5 157750554 750 0.97305 N/A PS123 rs6879366 0.00173 0.05286 T A GENE123 0.4014717125382263 5 157750669 750 0.97395 N/A PS123 rs75311988 0.35575 0.1246 T G GENE123 0.0316800458715595 5 157750814 750 0.0043008 N/A PS123
However, when I try
eqtl.df = formatColoc(fname = "myfile.txt", type="quant", N=750, Ncases=NA, info_filter=0.6, maf_filter=0.05, fread=T, eqtl=TRUE) I get:
eqtl.df = formatColoc(fname = "myfile.txt", type="quant", N=750, Ncases=NA, info_filter=0.6, maf_filter=0.05, fread=T, eqtl=TRUE)
Error in fread(fname, sep = "\t", select = colsAll[[1]], col.names = names(colsAll[[1]]), : colClasses is type 'integer' but should be list or character
Thanks in advance!
My data file looks like this:
However, when I try
eqtl.df = formatColoc(fname = "myfile.txt", type="quant", N=750, Ncases=NA, info_filter=0.6, maf_filter=0.05, fread=T, eqtl=TRUE)
I get:Thanks in advance!