fcnv-methods: Inference of functional CNVs

In diggit: Inference of Genetic Variants Driving Cellular Phenotypes

Description

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

Usage

fCNV(x, ...)

## S4 method for signature 'diggit'
fCNV(x, expset = NULL, cnv = NULL,
  method = c("spearman", "mi", "pearson", "kendall"), cores = 1,
  verbose = TRUE)

## S4 method for signature 'ExpressionSet'
fCNV(x, cnv, method = c("spearman", "mi", "pearson",
  "kendall"), cores = 1, verbose = TRUE)

## S4 method for signature 'matrix'
fCNV(x, cnv, method = c("spearman", "mi", "pearson",
  "kendall"), cores = 1, verbose = TRUE)

## S4 method for signature 'data.frame'
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]

diggit documentation built on Nov. 8, 2020, 8:18 p.m.