Stahl-Lab-MSSM / coloc2

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Error when reading input eqtl file: colClasses is type 'integer' but should be list or character #5

Open mocksu opened 1 year ago

mocksu commented 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:

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!