GSEPD_ChangeConditions

Description

This function is an interface to set which samples are the test conditions. Don't forget to GSEPD_Process() after changing settings. If you want to systematically try each condition pairing, try GSEPD_ProcessAll()

Usage

GSEPD_ChangeConditions(GSEPD, newConditions)

Arguments

Details

Interface will check if the conditions are known, then set the C2T value.

Value

Returns the GSEPD parameter object with its mode set via the C2T and Conditions element of the named list. These tell later steps which sample conditions you intend on comparing.

See Also

GSEPD_Example

Examples

  data("IlluminaBodymap")
  data("IlluminaBodymapMeta")
  set.seed(1000) #fixed randomness
  isoform_ids <- Name_to_RefSeq(c("HIF1A","EGFR","MYH7","CD33","BRCA2"))
  rows_of_interest <- unique( c( isoform_ids ,
                                 sample(rownames(IlluminaBodymap),
                                        size=500,replace=FALSE)))
  G <- GSEPD_INIT(Output_Folder="OUT",
                finalCounts=round(IlluminaBodymap[rows_of_interest , ]),
                sampleMeta=IlluminaBodymapMeta,
                COLORS=c("green","black","red"))
        ConditionsToTest <- c("A","B")
  G <- GSEPD_ChangeConditions( G, ConditionsToTest  )
  #G <- GSEPD_Process( G ) #would test samples A vs samples B
  G <- GSEPD_ChangeConditions( G, c("A","C"))
  #G <- GSEPD_Process( G ) #would test samples A vs samples C

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(rgsepd)
Loading required package: DESeq2
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

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


Attaching package: 'S4Vectors'

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

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: goseq
Loading required package: BiasedUrn
Loading required package: geneLenDataBase


Loading R/GSEPD 1.4.2
Building human gene name caches
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/rgsepd/GSEPD_ChangeConditions.Rd_%03d_medium.png", width=480, height=480)
> ### Name: GSEPD_ChangeConditions
> ### Title: GSEPD_ChangeConditions
> ### Aliases: GSEPD_ChangeConditions
> 
> ### ** Examples
> 
>   data("IlluminaBodymap")
>   data("IlluminaBodymapMeta")
>   set.seed(1000) #fixed randomness
>   isoform_ids <- Name_to_RefSeq(c("HIF1A","EGFR","MYH7","CD33","BRCA2"))
>   rows_of_interest <- unique( c( isoform_ids ,
+                                  sample(rownames(IlluminaBodymap),
+                                         size=500,replace=FALSE)))
>   G <- GSEPD_INIT(Output_Folder="OUT",
+                 finalCounts=round(IlluminaBodymap[rows_of_interest , ]),
+                 sampleMeta=IlluminaBodymapMeta,
+                 COLORS=c("green","black","red"))
Keeping rows with counts (458 of 505)
>         ConditionsToTest <- c("A","B")
>   G <- GSEPD_ChangeConditions( G, ConditionsToTest  )
>   #G <- GSEPD_Process( G ) #would test samples A vs samples B
>   G <- GSEPD_ChangeConditions( G, c("A","C"))
>   #G <- GSEPD_Process( G ) #would test samples A vs samples C
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>