filter_acset: Filter variants and features
In edsgard/scphaser: Phase Variants Within Genes Using Allele Counts

Description Usage Arguments Details Value Examples

filter_acset removes variants and features with too little data

1	filter_acset(acset, nmincells = 5, nminvar = 2, feat_filter = FALSE)

`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.
`nminvar`	An integer specifying the minimum number of variants within a feature.
`feat_filter`	Boolean specifying if filtering should be done per feature including an initial cell-filter removing cells with less than two variants with imbalanced expression within the feature.

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. Subsequently it removes features with less than "nminvar" variants, see filter_feat_nminvar.

acset An acset list.

##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 nmincells cells and
##features with less than nminvar variants
nmincells = 5
nminvar = 2
acset_filt = filter_acset(acset, nmincells, nminvar)