CnvGSAInput-class: Class '"CnvGSAInput"'

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

Description

Container class for the input structures required by the main function (i.e. cnvGSALogRegTest()).

Slots

config.ls:

Object of class "list" containing the file names and paths.

params.ls:

Object of class "list" containing the test parameters.

cnvData.ls:

Object of class "list" containing CNV data.

phData.ls:

Object of class "list" containing phenotype and covariate data.

gsData.ls:

Object of class "list" containing gene-set data.

geneID.ls:

Object of class "list" containing Gene ID data.

Constructor

CnvGSAInput( config.ls, params.ls, cnvData.ls, phData.ls, gsData.ls, geneID.ls): Creates a CnvGSAInput object.

config.ls

Structure containing the file names and paths.

params.ls

Structure containing main test parameters.

cnvData.ls

Structure containing CNV data along with sample-to-class information and filters.

phData.ls

Structure containing phenotype and covariate data.

gsData.ls

Structure containing gene-set data.

geneID.ls

Structure containing Gene ID data.

See the vignette for complete details on each of these structures as well as a full example of how to load them.

Methods

config.ls

signature(obj = "CnvGSAInput"): Gets config.ls.

config.ls<-

signature(obj = "CnvGSAInput"): Sets config.ls.

params.ls

signature(obj = "CnvGSAInput"): Gets params.ls.

params.ls<-

signature(obj = "CnvGSAInput"): Sets params.ls.

cnvData.ls

signature(obj = "CnvGSAInput"): Gets cnvData.ls.

cnvData.ls<-

signature(obj = "CnvGSAInput"): Sets cnvData.ls.

phData.ls

signature(obj = "CnvGSAInput"): Gets phData.ls.

phData.ls<-

signature(obj = "CnvGSAInput"): Sets phData.ls.

gsData.ls

signature(obj = "CnvGSAInput"): Gets gsData.ls.

gsData.ls<-

signature(obj = "CnvGSAInput"): Sets gsData.ls.

geneID.ls

signature(obj = "CnvGSAInput"): Gets geneID.ls.

geneID.ls<-

signature(obj = "CnvGSAInput"): Sets geneID.ls.

Author(s)

Joseph Lugo [e-mail]

Examples

## 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'brglm' will gradually be superseded by 'brglm2' (https://cran.r-project.org/package=brglm2), which provides utilities for mean and median bias reduction for all GLMs and methods for the detection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':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    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
Loading required package: data.table

Attaching package: 'data.table'

The following object is masked from 'package:GenomicRanges':

    shift

The following object is masked from 'package:IRanges':

    shift

The following objects are masked from 'package:S4Vectors':

    first, second

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