cnvGSAlogRegTest: Performing the logistic regression tests on the CNV data.

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

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

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

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

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'brglm' will gradually be superseded by 'brglm2' (https://cran.r-project.org/package=brglm2), which provides utilities for mean and median bias reduction for all GLMs and methods for the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