filter.samples: FALSEilter X, Y and genotype data by call rate

In DOQTL: Genotyping and QTL Mapping in DO Mice

Description

This function reads in "x.txt", "y.txt", "geno.txt" and "call.rate.batch.txt" from the user specified input directory and removes samples with a call rate less than the supplied threshold (default = 0.9). It then writes the files out to "x.filt.txt", "y.filt.txt", "geno.filt.txt" and "call.rate.batch.filt.txt".

Usage

  filter.samples(path = ".", thr = 0.9)

Arguments

path	Character, the full path to the directory where the files reside.
thr	Numeric, call rate threshold below which samples will be removed. Default = 0.9.

Value

data.frame with the sample IDs and call rates of the removed samples. The intensity and genotype files are written to the input directory.

Author(s)

Daniel Gatti

See Also

extract.raw.data, batch.normalize

Examples

  ## Not run: 
     filter.samples(path = "/tmpdir/output")
  
## End(Not run)

DOQTL documentation built on May 6, 2019, 3:09 a.m.