get.inframes: In-frame / out-of-frame sequences filter.

In imminfo/tcr: Advanced Data Analysis of Immune Receptor Repertoires

Description

Return the given data frame with in-frame or out-of-frame sequences only. Nucleotide sequences in a column "CDR3.nucleotide.sequence" are checked if they length are divisible by 3 (len mod 3 == 0 => in-frame, else out-of-frame)

Usage

get.inframes(.data, .head = 0, .coding = T)

get.outframes(.data, .head = 0)

count.inframes(.data, .head = 0, .coding = T)

count.outframes(.data, .head = 0)

get.frames(.data, .frame = c('in', 'out', 'all'), .head = 0, .coding = T)

count.frames(.data, .frame = c('in', 'out', 'all'), .head = 0, .coding = T)

Arguments

.data	MiTCR data.frame or a list with mitcr data.frames.
.head	Parameter to the head() function. Supply 0 to get all elements. head applied before subsetting, i.e. if .head == 500, you will get in-frames from the top 500 clonotypes.
.coding	if T then return only coding sequences, i.e. without stop-codon.
.frame	Which *-frames to choose.

Value

Filtered data.frame or a list with such data.frames.

imminfo/tcr documentation built on June 13, 2020, 7:01 a.m.