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 |
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.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 | ##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)
|
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