Performing the logistic regression tests on the CNV data.

Description

This test uses 4 different correction models and requires a case control study. It looks at odds ratios and calculates statistics for the gene-set collection.

Usage

cnvGSAlogRegTest(cnvGSA.in, cnvGSA.out)

Arguments

Value

A list of one or two objects depending on whether or not the user includes the known loci in the analysis. Each object in the list contains the regression results for each gene set.

Examples

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

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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Type 'demo()' for some demos, 'help()' for on-line help, or
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> library(cnvGSA)
Loading required package: brglm
Loading required package: profileModel
Loading required package: doParallel
Loading required package: foreach
Loading required package: iterators
Loading required package: parallel
Loading required package: GenomicRanges
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, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, 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, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

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

    colMeans, colSums, expand.grid, rowMeans, rowSums

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

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/cnvGSA/cnvGSAlogRegTest.Rd_%03d_medium.png", width=480, height=480)
> ### Name: cnvGSAlogRegTest
> ### Title: Performing the logistic regression tests on the CNV data.
> ### Aliases: cnvGSAlogRegTest
> 
> ### ** Examples
> 
> library(cnvGSAdata)
> data(cnvGSA_output_example)
> ## See vignette for full details and worked example
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>