filter.samples {DOQTL} | R Documentation

## FALSEilter X, Y and genotype data by call rate

### 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)

[Package DOQTL version 1.16.2 Index]