call_gt: Call transcribed genotypes

Description Usage Arguments Details Value Examples

Description

call_gt calls transcribed genotypes using allele RNA-seq read counts

Usage

1
call_gt(acset, min_acount = 3, fc = 3)

Arguments

acset

An acset list created by the function new_acset. The acset must contain a refcount and altcount matrix with allele counts.

min_acount

An integer specifying the minimum number of reads required to be present for at least one of the two alleles as to make a call. If not fulfilled the call is set to NA.

fc

An integer specifying the fold-change cutoff between the expression of the alternative and reference allele (fc.observed = alternative allele count / reference allele count). The transcribed genotype call is set to 0 if fc.observed <= fc, 2 if fc.observed >= fc and 1 otherwise (if there are enough reads present, see the "min_acount" parameter).

Details

This is a simplistic transcribed genotype caller which is used to discretize which allele is the most expressed. For each variant and cell one of four possible discrete values is set depending on the expression of the two alleles. 0: reference allele most highly expressed, 1: bi-allelic expression with similar degree of expression from the two alleles, 2: alternative allele most highly expressed, or, NA if there are not enough reads to make a call.

Value

acset An acset list where the "gt" element is set or updated. "gt" is a matrix with integer values representing transcribed genotype calls. 0: reference allele most highly expressed, 1: bi-allelic expression with similar degree of expression from the two alleles, 2: alternative allele most highly expressed. NA's are used to represent entries where no call could be made. The rownames are set to the variant column, "var", of featdata. The colnames are set to the colnames of "refcount". The elements [['args']][['filter']][c('min_acount', 'fc')] are added or updated to the acset as to record the filter arguments used.

Examples

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
##load dataset
invisible(marinov)
acset = new_acset(featdata = marinov[['featdata']], refcount =
marinov[['refcount']], altcount = marinov[['altcount']], phenodata =
marinov[['phenodata']])

##Call transcribed genotypes
min_acount = 3
fc = 3
acset = call_gt(acset, min_acount, fc)

edsgard/scphaser documentation built on May 15, 2019, 11:02 p.m.