compute_rearr_stat_dist: Computes distances between samples in a dataset based on...

Description Usage Arguments Value

View source: R/batch.R

Description

Produces a data frame with pairwise distances between samples computed for segment usage, insert size and segment trimming size histograms. A square root of Jensen-Shannon Divergence is used as a metric. Note that no distances are computed for samples having distinct antigen receptor chain lists

Usage

1
2
compute_rearr_stat_dist(stats_bundle, value.types = c("reads", "clonotypes"),
  add.pseudocounts = F, cores = 2)

Arguments

stats_bundle

a set of rearrangement statistics produced by 'compute_rearr_stats' function

value.types

specifies whether to use weighted histograms - 'reads' or to count each clonotype once - 'clonotypes'; can specify both

add.pseudocounts

if true will re-compute histograms by adding a pseudocount of 1 to each histogram, including missing bins, and re-normalize them to new total

cores

number of cores for parallelization

Value

a data frame holding pairwise distances between samples for each rearrangement statistic


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