Reading in the config file.

Description

This function is used to read in all the values from the config file and change them in the S4 objects used throughout the scripts. If you would like to reload the config values, you will want to run this function.

Usage

f.readConfig(configFile, cnvGSA.in)

Arguments

Value

A CnvGSAInput object with the updated config.ls and params.ls objects.

Examples

library(cnvGSAdata)
data(cnvGSA_input_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/f.readConfig.Rd_%03d_medium.png", width=480, height=480)
> ### Name: f.readConfig
> ### Title: Reading in the config file.
> ### Aliases: f.readConfig
> 
> ### ** Examples
> 
> library(cnvGSAdata)
> data(cnvGSA_input_example)
> ## See vignette for full details and worked example
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>