GBSA: Averaging the called sites into customised bins.

In yanjunzan/GBSA: Genotype imputation and QTL mapping with ultra low coverage sequencing in pedigree

Description

Given intermediated files generated by format_grand.p or read.trio, this function bin the genome to consecutive bins and average gentoype calls across differnt bin

Usage

GBSA(cutoffLevel,pedigreeTable,matchingNames,bin.size,vcf.file.f2,pathout,py.script)

Arguments

cutoffLevel	The number of markers in each bin. Below this cutoff this bin is marked as NA,otherwise average is not used as calls
pedigreeTable	a data.frame with 7 columns with names as id.f2, id.f2.ma, id.f2.fa, fa.h, ma.h, ma.l, fa.l. Those are F2 id, corresponding mother id,father id and grand parent ids, fa.h,ma.h must come from one line and ma.l, fa.l. from another divergent line
matchingNames	a tab delimited file,documenting the chrmsome name length and contig names, see examples:https://github.com/yanjunzan/F2_re_seq/blob/master/data/chr_id.match.txt only columns: RefSeq,INSDC,Type,Name,Size(Mb) are necessary
bin.size	how large the size of the bin should be
vcf.file.f2	input vcf file
pathout	path to the directory where intermediate files are stored

Value

return a data.table object with genotypes of each bin in column and individuals in each row.

Author(s)

Yanjun Zan, Thibaut Payen

References

Yanjun Zan, Thibaut Payen, Leif Andersson, Paul B. Siegel and <c3><96>rjan Carlborg;Whole-genome QTL mapping in experimental pedigrees from outbred founders utilizing low coverage individual based sequencing 2018

yanjunzan/GBSA documentation built on May 14, 2019, 4:05 a.m.