Description Usage Arguments Details Value Examples
racset
randomizes the entries in the allele count matrixes or the
genotype matrix
1 |
acset |
An acset list created by |
type |
A character string with two allowed values. 'ac' specifies that the allele count matrixes should be randomized and 'gt' specifies that the genotype matrix should be randomized. |
fixedrowmargin |
Boolean specifying if the row-sums should be kept unchanged. |
The function scrambles all entries within each allele count matrix or within the genotype matrix.
acset A randomized acset list.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 | ##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)
##Randomize the genotype matrix
type = 'gt'
acset_rand = racset(acset, type)
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