subset_cols: Subset cells

In edsgard/scphaser: Phase Variants Within Genes Using Allele Counts

Description

subset_cols subsets the cells of an acset

Usage

subset_cols(acset, sel.ind)

Arguments

acset	An acset list created by the new_acset function.
sel.ind	A vector with either integer column indices or a character vector to subset the colnames.

Value

acset An acset list where every element containing cell-related information has been subsetted

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)

##subset variants
sel_ind = c(1, 3)
acset = subset_cols(acset, sel_ind)

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