bioinformatics-ptp/detectRUNS

Deal with tab-separated ped files

Opened this issue · 1 comments

bunop commented

Is your feature request related to a problem? Please describe.
As described in #9, slidingRUNS.run cannot handle tab separated files. Change code and try to deal with tab separate files or add a warning to the user

Describe the solution you'd like
Deal with both Tab Separated Files and Space Separated Files (and even the binary format if possible)

Describe alternatives you've considered
We could simply state that the Space Separated format is the only supported format in our vignettes and documentation

Additional context

  • Clearly state that the only supported format is the Space Separated

or

  • fix both genotype <- (strsplit(oneLine, " ")) in consecutiveRUNS.run and slidingRUNS.run
  • fix readPOPCpp() to read also TSV files (a s described in #15)
  • support for binary format?
filippob commented

In the meanwhile, tab-separated Plink files can be converted to space-separated files within Plink using the --recode option, which under Plink 1.9 should produce space-separated files, or forcing this explicitly with the spacex option (details here: Plink data management)

Alternatively, tab-delimited files can be converted to space-delimited files in R (e.g. data.table::fread/fwrite), or using bash commands (e.g. sed)