tcR (version 1.1)

get.deletions.alpha: Compute the number of deletions in MiTCR data frames.

Description

Get deletions for VD, DJ, 5'D and 3'D ends and two columns with total deletions for VD/DJ and 5'D/3'D deletions for the given mitcr data.frame with 0-indexes columns. Cases, in which deletions cannot be determined, will have -1 in their cell.

Usage

get.deletions.alpha(.data, .Vs = segments$TRAV, .Js = segments$TRAJ)
get.deletions.beta(.data, .Vs = segments$TRBV, .Js = segments$TRBJ, .Ds = segments$TRBD)

Arguments

.data

Mitcr data.frame.

.Vs

Table of V segments; must have 'V.segment' and 'Nucleotide.sequence' columns.

.Js

Table of J segments; must have 'J.segment' and 'Nucleotide.sequence' columns.

.Ds

Table of D segments; must have 'D.segment' and 'Nucleotide.sequence' columns.

Value

• Mitcr data.frame with 3 (for alpha chains) or 5 (for beta chains) new columns for deletions.

Details

By default, *.table parameters are taken from the segments data frame which can be loaded to your R environment with data(segments). Data for segments has been taken from IMGT.

Examples

data(segments)
immdata <- get.deletions.beta(.data)
immdata.prob <- tcr.prob.df(immdata)