tcR (version 2.2.4)

entropy.seg: Repertoires' analysis using information measures applied to V- and J- segment frequencies.

Description

Information approach to repertoire analysis. Function entropy.seg applies Shannon entropy to V-usage and hence measures variability of V-usage. Function js.div.seg applied Jensen-Shannon divergence to V-usage of two or more data frames and hence measures distance among this V-usages.

Usage

entropy.seg(.data, .genes = HUMAN_TRBV, .frame = c('all', 'in', 'out'),
            .quant = c(NA, "read.count", "umi.count", "read.prop", "umi.prop"),
            .ambig = F)
js.div.seg(.data, .genes = HUMAN_TRBV, .frame = c('all', 'in', 'out'),
           .quant = c(NA, "read.count", "umi.count", "read.prop", "umi.prop"),
           .norm.entropy = T, .ambig = F, .verbose = F, .data2 = NULL)

Arguments

.data

Mitcr data.frame or a list with mitcr data.frames.

.genes

Parameter to the geneUsage function.

.frame

Character vector of length 1 specified which *-frames should be used: only in-frame ('in'), out-of-frame ('out') or all sequences ('all').

.quant

Which column to use for the quantity of clonotypes: NA for computing only number of genes without using clonotype counts, "read.count" for the "Read.count" column, "umi.count" for the "Umi.count" column, "read.prop" for the "Read.proportion" column, "umi.prop" for the "Umi.proportion" column.

.ambig

Parameter passed to geneUsage.

.data2

NULL if .data is a list, or a second mitcr data.frame.

.norm.entropy

if T then divide result by mean entropy of 2 segments' frequencies.

.verbose

If T than output the data processing progress bar.

Value

For entropy.seg - numeric integer with entropy value(s). For js.div.seg - integer of vector one if .data and .data2 are provided; esle matrix length(.data) X length(.data) if .data is a list.

See Also

vis.heatmap, vis.group.boxplot, geneUsage