entropy.seg: Repertoires' analysis using information measures applied to...
In tcR: Advanced Data Analysis of Immune Receptor Repertoires

Description Usage Arguments Value See Also

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.

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)

`.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.

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.

vis.heatmap, vis.group.boxplot, geneUsage

tcR documentation built on July 2, 2020, 3:18 a.m.