Subsetting a "DEXUSResult".

Description

Information about specific transcripts can be accessed in the "DEXUSResult" object by using the standard brackets "[idx]" for subsetting. Either transcript names or transcript indices can be used.

Arguments

Value

An instance of "DEXUSResult".

Author(s)

Guenter Klambauer klambauer@bioinf.jku.at and Thomas Unterthiner unterthiner@bioinf.jku.at

Examples

data(dexus)
res <- dexus(countsBottomly[1:100, ])
res["ENSMUSG00000000486"]
res[50:55]

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(dexus)
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: 'dexus'

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

    sizeFactors

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/dexus/DEXUSResult-subset.Rd_%03d_medium.png", width=480, height=480)
> ### Name: `[`
> ### Title: Subsetting a "DEXUSResult".
> ### Aliases: `[` `[`,DEXUSResult,character-method
> ###   `[`,DEXUSResult,logical-method `[`,DEXUSResult,numeric-method
> 
> ### ** Examples
> 
> data(dexus)
> res <- dexus(countsBottomly[1:100, ])
Filtered out 5 % of the genes due to low counts
Unsupervised mode.
> res["ENSMUSG00000000486"]
Displaying the 10 top ranked genes of the analyis: 
  Index         Transcript INIcall   INI Mean.Condition_1 Mean.Condition_2
1     1 ENSMUSG00000000486    TRUE 0.351              9.7              2.1

Total number of transcripts:  1 
Number of differentially expressed transcripts:  1 
Percentage of differentially expressed transcripts:  100 % 
> res[50:55]
Displaying the 10 top ranked genes of the analyis: 
  Index         Transcript INIcall   INI Mean.Condition_1 Mean.Condition_2
1     1 ENSMUSG00000000282   FALSE 0.053            378.5            588.0
2     5 ENSMUSG00000000301   FALSE 0.000             12.6              1.8
3     6 ENSMUSG00000000303   FALSE 0.000             17.7             10.6
4     2 ENSMUSG00000000290   FALSE 0.000             41.5             36.9
5     4 ENSMUSG00000000296   FALSE 0.000            248.7            241.0
6     3 ENSMUSG00000000295   FALSE 0.000             63.6             61.7

Total number of transcripts:  6 
Number of differentially expressed transcripts:  0 
Percentage of differentially expressed transcripts:  0 % 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>