segment2_usage_dist: Compute the pairwise Jensen-Shannon distance between samples...
In milaboratory/mirutil:

Computes pairwise set of Jensen-Shannon distance provided a set of segment pair usage histograms. If specified, will also only compare samples with the same antigen receptor chain

1 2	segment2_usage_dist(data, value.types = c("reads", "clonotypes"), add.pseudocounts = F, cores = 2, filter.by.chain = F)

`data`	a set of histograms produced by 'compute_segment_usage2' function
`add.pseudocounts`	if True, will add pseudocounts and re-normalize histograms, in this case 'value' should contain count, not frequency
`cores`	number of cores for parallelization
`filter.by.chain`	if True, will only compare samples with the same chain, requires additional 'chain' column in 'data'

a pairwise distance table, containing sample ids in 'sample.id.1' and 'sample.id.2' columns, statistic type in 'type' column and distance in 'd' column; if 'filter.by.chain' is set to true will also include 'chain' column

milaboratory/mirutil documentation built on May 20, 2019, 1:24 p.m.