humanGeneInput: Example human gene data

In GeneAnswers: Integrated Interpretation of Genes

Description

An example of a group of human gene data.

Usage

data(humanGeneInput)

Format

A data frame with 86 observations. Column names are "Symbol", "foldChange" and "pValue". Row names are gene Entrez IDs. For general usage, row names of geneInput could be anything.

Details

Fold change could be negative, which means the ratio of treatment to control is less than 1 and the value is reciprocal of general fold change.

References

Feng, G., Du, P., Krett, N., Tessel, M., Rosen, S., Kibbe, W.A. and Lin, S.M., 'A collection of bioconductor methods to visualize gene-list annotations', BMC Research Notes 2010, 3:10

Examples

data(humanGeneInput)
humanGeneInput[1:10,]

Example output

Loading required package: igraph

Attaching package: 'igraph'

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

    decompose, spectrum

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

    union

Loading required package: RCurl
Loading required package: bitops
Loading required package: annotate
Loading required package: AnnotationDbi
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:igraph':

    normalize, union

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: 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: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    expand.grid

Loading required package: XML
Loading required package: RSQLite
Loading required package: MASS

Attaching package: 'MASS'

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

    select

Loading required package: Heatplus
Loading required package: RColorBrewer
Warning messages:
1: replacing previous import 'stats::decompose' by 'igraph::decompose' when loading 'GeneAnswers' 
2: replacing previous import 'stats::spectrum' by 'igraph::spectrum' when loading 'GeneAnswers' 
      GeneID foldChange       pValue
374      374  17.553825 1.241073e-11
2289    2289  10.549139 5.513686e-14
10563  10563  10.688601 1.073456e-10
687      687   6.112663 1.351898e-09
80149  80149   4.939585 6.473841e-09
5033    5033   4.265287 1.341238e-06
7088    7088   5.427252 1.993568e-11
64764  64764   2.909868 1.162846e-08
10628  10628   3.899457 4.296784e-09
5087    5087   2.552036 1.120693e-07

GeneAnswers documentation built on Nov. 8, 2020, 4:53 p.m.