classMat: Classification matrix estimating accuracy of model.

In BioHPC/iCAT: immune Cell Analysis Tool

Description

Classification matrix estimating accuracy of model.

Usage

classMat(comb)

Arguments

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

Value

Matrix with % correct predictions from 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", "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)
classMat(mod)

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