tcR (version 1.3)

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

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 than 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.