trnStats: Statistics about training data.

In BioHPC/iCAT: immune Cell Analysis Tool

Description

Statistics about training data.

Usage

trnStats(listPre, listPost, field, count, copyrange)

Arguments

listPre	Vector of negative training samples.
listPost	Vector of positive training samples.
field	String containing the column or columns (space-delimited) of interest.
count	String containing the column name for colontype counts.
copyrange	Integer Vector of the min and max copy of a sequence, within a sample, to be considered.

Value

Dataframe containing number of samples, colonotypes, and unique seqs in training data.

Examples

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

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

trnStats(listPos, listNeg, FIELD, COUNT, COPY_RANGE)

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