tcR (version 1.0)

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, .frame = c('all', 'in', 'out'),
            .alphabet = if (.VJ) "beta" else 'TRBV', .meat = F, .other = T, .VJ = F)
js.div.seg(.data, .data2 = NULL, .frame = c('all', 'in', 'out'), .norm.entropy = T,
           .alphabet = if (.VJ) "beta" else 'TRBV', .meat = F, .other = T, .VJ = F,
           .verbose = T)

Arguments

.data

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

.frame

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

.alphabet

Parameter to freq.segments() and freq.segments.2D() functions.

.meat

Parameter to freq.segments() and freq.segments.2D() functions.

.other

Parameter to freq.segments() and freq.segments.2D() functions.

.VJ

If F than apply freq.segments function, else apply freq.segments.2D function.

.data2

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

.norm.entropy

If T than divide result by mean entropy of 2 segments' frequencies.

.verbose

If T than print progress of function executing.

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, freq.segments