diggit (version 1.4.0)

fCNV: Inference of functional CNVs

Description

This function infers functional CNVs by computing their association with gene expression

Usage

fCNV(x, ...)
"fCNV"(x, expset = NULL, cnv = NULL, method = c("spearman", "mi", "pearson", "kendall"), cores = 1, verbose = TRUE)
"fCNV"(x, cnv, method = c("spearman", "mi", "pearson", "kendall"), cores = 1, verbose = TRUE)
"fCNV"(x, cnv, method = c("spearman", "mi", "pearson", "kendall"), cores = 1, verbose = TRUE)
"fCNV"(x, cnv, method = c("spearman", "mi", "pearson", "kendall"), cores = 1, verbose = TRUE)

Arguments

x

Object of class diggit, expressionSet object or numeric matrix of expression data, with features in rows and samples in columns

...

Additional arguments

expset

Optional numeric matrix of expression data

cnv

Optional numeric matrix of CNVs

method

Character string indicating the method for computing the association between CNVs and expression

cores

Integer indicating the number of cores to use (1 for Windows-based systems)

verbose

Logical, whether to report analysis progress

Value

Objet of class diggit with updated fCNV slot

Examples

data(gbm.expression, package="diggitdata")
data(gbm.cnv, package="diggitdata")
genes <- intersect(rownames(gbmExprs), rownames(gbmCNV))[1:100]
gbmCNV <- gbmCNV[match(genes, rownames(gbmCNV)), ]
dgo <- diggitClass(expset=gbmExprs, cnv=gbmCNV)

dgo <- fCNV(dgo)
dgo
diggitFcnv(dgo)[1:5]
dgo <- fCNV(gbmExprs, gbmCNV)
print(dgo)
diggitFcnv(dgo)[1:5]
dgo <- fCNV(exprs(gbmExprs), gbmCNV)
dgo
diggitFcnv(dgo)[1:5]
dgo <- fCNV(as.data.frame(exprs(gbmExprs)), gbmCNV)
dgo
diggitFcnv(dgo)[1:5]