readTrn: Read input training data.

In BioHPC/iCAT: immune Cell Analysis Tool

Description

Read input training data.

Usage

readTrn(list, field, count, copyrange, posOrNeg)

Arguments

list	Vector of training samples.
field	String containing the column or columns (space-delimited) of interest.
count	String containing the column name for colontype counts.
copyrange	Integer of the minimum copy of a sequence, within a sample, to be considered.
posOrNeg	String indicating whether the data is negative or positive.

Value

Dataframe containing unique sequences and their frequencies in the samples.

Examples

FIELD <- "vGeneName aminoAcid jGeneName"
COUNT <- "copy"
P_CUTOFF <- 0.1
MIN_PUBLIC <- 2
COPY_RANGE <- "1 99"

listPos <- tsvDir(system.file("extdata", "Post", package="iCAT"))
listNeg <- tsvDir(system.file("extdata", "Pre", package="iCAT"))

naive <- readTrn(listNeg, FIELD, COUNT, COPY_RANGE, "naive")
vaccs <- readTrn(listPos, FIELD, COUNT, COPY_RANGE, "vacc")

BioHPC/iCAT documentation built on Oct. 30, 2021, 3:12 p.m.