Extract_all: Extract the imputed genotypes and compile it into a...
In yanjunzan/TD: This is a R package processing output from TIGER pipeline.

Description Usage Arguments Value Author(s) References See Also

In this matrix, each row represents one individual and each column a block in the genome in which no crossover event was identified in the population.

1	Extract_all(chromosome = chr,id_all = id_all,all_vcf = all_vcf,gap=3e6,filter = T )

`id_all`	the Id of all the individuals after TIGER run
`filter`	if the double recombination within a certain distance(gap) should be filtered
`all_vcf`	links to the TIGER output
`chromosome`	all the chromsomes in TIGER run
`gap`	genotype swithing twich within this distance will be filtered out

return a genotype matrix, with the first two rows representing chr and mid-pos the bins. Starting from the third row, each row represents one individual and each column is a block in the genome in which no crossover event was identified in the population.

Yanjun Zan, Thibaut Payen

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

Extract_co_all_chr

yanjunzan/TD documentation built on May 18, 2019, 3:40 a.m.