cnvGSAgsTables: Creates the gene-set tables for each gene-set.

In cnvGSA: Gene Set Analysis of (Rare) Copy Number Variants

Description

Creates the gene-set tables for each gene-set.

Usage

cnvGSAgsTables(cnvGSA.in, cnvGSA.out)

Arguments

cnvGSA.in	A CnvGSAInput S4 object.
cnvGSA.out	A CnvGSAOutput S4 object.

Value

A list where each object is a table corresponding to one gene-set.

Examples

library(cnvGSAdata)
data(cnvGSA_output_example)
## See vignette for full details and worked example

Example output

Loading required package: brglm
Loading required package: profileModel
'brglm' will gradually be superseded by 'brglm2' (https://cran.r-project.org/package=brglm2), which provides utilities for mean and median bias reduction for all GLMs and methods for the detection of infinite estimates in binomial-response models.
Loading required package: doParallel
Loading required package: foreach
Loading required package: iterators
Loading required package: parallel
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, basename, cbind, colnames,
    dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
    grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
    rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: ‘S4Vectors’

The following object is masked from ‘package:base’:

    expand.grid

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: splitstackshape

cnvGSA documentation built on Nov. 8, 2020, 5:04 p.m.