plotHist: Plot histogram of clonotype frequencies in negative and...

Description Usage Arguments Value Examples

View source: R/plotHist.R

Description

Plot histogram of clonotype frequencies in negative and positive samples.

Usage

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plotHist(comb)

Arguments

comb

List containing both negtive (n) and positive (v) clonotype percentages.

Value

ggplot histogram of clonotype frequencies in negative and positive samples

Examples

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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")  

mod <- train(naive, vaccs, listNeg, listPos, FIELD, COUNT, COPY_RANGE, P_CUTOFF, MIN_PUBLIC, NULL)
plotHist(mod)

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