filter.samples


    Character, the full path to the directory where the files reside.
  

path


    Numeric, call rate threshold below which samples will be removed. Default = 0.9.
  


  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".


 normalization

 MUGA 

 call rate 

DOQTL is a quantitative trait locus (QTL) mapping pipeline designed for Diversity Outbred mice and other multi-parent outbred populations. The package reads in data from genotyping arrays and perform haplotype reconstruction using a hidden Markov model (HMM). The haplotype probabilities from the HMM are then used to perform linkage mapping. When founder sequences are available, DOQTL can use the haplotype reconstructions to impute the founder sequences onto DO genomes and perform association mapping.

Daniel Gatti

DOQTL

Genotyping and QTL Mapping in DO Mice

filter.samples function

Character, the full path to the directory where the files reside.

Numeric, call rate threshold below which samples will be removed. Default = 0.9.

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".

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

Description

Usage

Arguments

Value

See Also

Examples