fdrMatrix: Retrieve FDR matrix

In hshdndx/new-to-CNV: patternCNV: a versatile tool for detecting copy number changes from exome-seq data

Description

This function retrieves a data matrix of p-value or FDR from an object of PatCNVData-class.

Usage

fdrMatrix(obj, sample.name = NULL, gene.name = NULL, 
          chr = NULL, pos.range = NULL, exon.score.vec = NULL,
          min.exon.score = NULL, capture.only = FALSE, 
          type = "FDR", exon.ID.format = "gene+pos")

Arguments

obj	an object of PatCNVData-class
sample.name	a character vector containing sample names. A value of NULL instructs the function to select all the samples
gene.name	a character vector containing gene names. A value of NULL instructs the function to select all the genes
chr	selected chromosome
pos.range	a numeric vector of two values indicating start and end positions of selected chromosome
exon.score.vec	a numeric vector of per-exon confidence score
min.exon.score	minimum exon confidence score
capture.only	a logical value indicating if only captured exons should be used
type	"FDR" or "pval". Default value "FDR" refers to false discovery rate and "pval" refers to nominal p-value
exon.ID.format	"gene+pos" or "pos" indicating how to format exon IDs

Value

an FDR/p-value matrix of exon by sample

Author(s)

Chen Wang

See Also

estimateFDR, fitNullModel

Examples

#=== load simulated data with pre-computed coverage and CNV
data(sim.cnvData)

#=== fit null distribution of CNV signals and plot distribution
null.model <- fitNullModel(sim.cnvData, "all")
germline.data <- estimateFDR(sim.cnvData, null.model)

#=== list FDR of a few top exons of samples "n2" and "n5"
head(fdrMatrix(germline.data,c("n2","n5")))

hshdndx/new-to-CNV documentation built on May 17, 2019, 5:55 p.m.