RcadeSTAT1: Rcade object - STAT1 data

In Rcade: R-based analysis of ChIP-seq And Differential Expression - a tool for integrating a count-based ChIP-seq analysis with differential expression summary data

Description

The Rcade object generated in the vignette, vignette("Rcade").

Usage

data(RcadeSTAT1)

Format

Object of Rcade class.

Source

Differential Expression data from Array Express, http://www.ebi.ac.uk/arrayexpress, under accession number E-GEOD-11299.

STAT1 ChIP-seq data from the Snyder lab, as part of the ENCODE consortium\ Input DCC accession numbers: wgEncodeEH000611 and wgEncodeEH000612\ ChIP DCC accession number: wgEncodeEH000614

Examples

data(RcadeSTAT1)
RcadeSTAT1
## maybe str(RcadeSTAT1) ; plot(RcadeSTAT1) ...

Example output

Loading required package: GenomicRanges
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, sd, var, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, 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, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    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: Rsamtools
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

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

    strsplit

Loading required package: baySeq
Loading required package: abind
Welcome to Rcade - version 1.18.0
If you are new to Rcade, please consider reading the vignette through the command: vignette("Rcade").

Attaching package: 'Rcade'

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

    plotPCA

Warning messages:
1: In rgl.init(initValue, onlyNULL) : RGL: unable to open X11 display
2: 'rgl_init' failed, running with rgl.useNULL = TRUE 
3: .onUnload failed in unloadNamespace() for 'rgl', details:
  call: fun(...)
  error: object 'rgl_quit' not found 
Rcade: 57 rows, 15 columns.
DE: 59 rows, 13 columns.
ChIP: 1 track(s):
[[1]]
annoZones: GRanges with 48 ranges and 1 elementMetadata col.
shift:0 
counts: 48 rows, 4 columns.
summary: 48 rows, 4 columns.

Metadata:
ChIPtargets: 4 rows, 5 columns.
fileDir:/home/cairnsj/R/x86_64-pc-linux-gnu-library/3.1/Rcade/extdata/STAT1

Rcade documentation built on Nov. 8, 2020, 6:25 p.m.