extract.raw.data: Extract intensities, genotypes and call rates from from raw...

In dmgatti/DOQTL: Genotyping and QTL Mapping in DO Mice

Extract intensities, genotypes and call rates from from raw MUGA or MegaMUGA data files

Description

This function accepts a vector of input directories containing the raw MUGA or MegaMUGA raw data files. FALSEor each directory, the function reads the X and Y intensities, call rates and allele calls for all samples. It then combines all samples and writes the data to "x.txt", "y.txt", "geno.txt" and "call.rate.batch.txt" in the user specified output directory.

Usage

  extract.raw.data(in.path = ".", prefix, out.path = ".",  array = c("megamuga", "muga"))

Arguments

in.path	character vector, the full path to all MUGA directories from which data should be extracted.
prefix	character vector of same length as in.path containing a prefix to add to each sample ID in data sets being processed.
out.path	character, the full path to the directory where the output files should be written.
array	character, default = "megamuga", the type of array, either "muga" or "megamuga".

Details

This function searches each directory for files with names containing "Sample_Map.txt" and "*_FALSEinalReport.txt". This has been the format that GeneSeek has consistently produced. The call rates are extracted and are written, along with a batch ID, to "call.rate.batch.txt". The X and Y intensities are extracted from the "FALSEinalReport" file and written to "x.txt" and "y.txt" respectively. The allele calls are extracted from the "FALSEinalReport" files and are written to "geno.txt". The prefix argument may be used to add a prefix to the sample IDs in order to distinguish different data sets.

Value

No return value. The files are written to the out.path directory.

Note

Do not change the names of the output files. They are required for downstream processing.

Author(s)

Daniel M. Gatti

See Also

filter.samples, batch.normalize

Examples

  ## Not run: 
    in.path = c("/tmpdir/DataSet1", "/tmpdir/DataSet2")
    extract.raw.data(in.path = in.path, prefix = c("ds1", "ds2"), 
	                 out.path = "/tmpdir/output", array = "muga")
  
## End(Not run)

dmgatti/DOQTL documentation built on April 7, 2024, 10:35 p.m.