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: "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.

Description

Usage

Arguments

Value

See Also