filter_var_gt: Filter variants

In scphaser: Phase Variants Within Genes Using Allele Counts

Description

filter_var_gt removes variants based on the number of cells with imbalanced expression

Usage

filter_var_gt(acset, nmincells = 3)

Arguments

acset	An acset list created by new_acset. It must contain a "gt" element with transcribed genotype calls, see call_gt.
nmincells	An integer specifying the minimum number of cells with imbalanced allelic expression.

Details

The function removes variants which have less than "nmincells" cells with imbalanced allelic expression. A cell is deemed to have imbalanced allelic expression if its transcribed genotype is set to 0 or 2, see call_gt.

Value

acset An acset list subsetted on variants that pass the filter.

Examples

##create a small artificial genotype matrix
ncells = 10
paternal = c(0, 2, 0, 0, 2)
maternal = c(2, 0, 2, 2, 0)
gt = as.matrix(as.data.frame(rep(list(paternal, maternal), ncells / 2)))
vars = 1:nrow(gt)
colnames(gt) = 1:ncells
rownames(gt) = vars

##create a feature annotation data-frame
nvars = nrow(gt)
featdata = as.data.frame(matrix(cbind(rep('jfeat', nvars),
as.character(1:nvars), rep('dummy', nvars), rep('dummy', nvars)), ncol = 4,
dimnames = list(vars, c('feat', 'var', 'ref', 'alt'))), stringsAsFactors =
FALSE)

##create acset
acset = new_acset(featdata, gt = gt)

##Remove variants with imbalanced expression in less than 3 cells
nmincells = 3
acset_filt = filter_var_gt(acset, nmincells)

scphaser documentation built on May 29, 2017, 3:49 p.m.