fpkm: Example RNA-seq data set.

In epigenomix: Epigenetic and gene transcription data normalization and integration with mixture models

Description

The data.frame stores transcription values obtained from the Cufflinks software for two samples (CEBPA_WT and CEBPA_KO). Transcription values are given in fragments per kilobase of transcripts per million fragments (FPKM).

Usage

data(fpkm)

Format

An object of class data.frame.

Details

All transcripts sharing the TSS were grouped and one transcription values is given for each group of transcripts. The example data contains a subset of about 3500 TSS located on chromosome 1.

Examples

data(fpkm)
head(fpkm)

Example output

Loading required package: Biobase
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, basename, cbind, colMeans, colSums, colnames,
    dirname, 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

Welcome to Bioconductor

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

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

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

    expand.grid

Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: 'matrixStats'

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

    anyMissing, rowMedians


Attaching package: 'DelayedArray'

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

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

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

    apply

Warning messages:
1: no function found corresponding to methods exports from 'DelayedArray' for: 'acbind', 'arbind' 
2: no function found corresponding to methods exports from 'SummarizedExperiment' for: 'acbind', 'arbind' 
    tracking_id     gene_id gene_short_name                 locus    CEBPA_WT
4       TSS1000 XLOC_000367        SH3BGRL3   1:26605666-26647014 9.01200e+00
16     TSS10001 XLOC_003811           TMCO1 1:165696031-165880855 1.27733e+02
38     TSS10003 XLOC_003811           TMCO1 1:165696031-165880855 5.63118e-02
49     TSS10004 XLOC_003812   RP11-525G13.2 1:165696031-165880855 1.08156e+00
82     TSS10007 XLOC_003814          FAM78B 1:166026673-166136206 1.60972e-03
149    TSS10013 XLOC_003815     RP11-9L18.2 1:166244865-166246834 1.15553e+00
       CEBPA_KO   tss_id
4   6.54111e+01  TSS1000
16  1.55132e+02 TSS10001
38  5.08823e-02 TSS10003
49  8.27812e-01 TSS10004
82  2.34348e-03 TSS10007
149 1.48034e+00 TSS10013
                                                                               ensemble.estid
4                                                                           ENST00000319041.6
16  ENST00000392129.6,ENST00000464650.1,ENST00000476143.2,ENST00000481278.1,ENST00000465705.1
38                                                       ENSG00000143183.12,ENST00000580248.1
49                                                        ENST00000455257.1,ENSG00000236364.1
82                                                        ENSG00000188859.5,ENST00000338353.3
149                                                       ENST00000400979.2,ENSG00000215835.2
    chr     start       end strand       tss
4     1  26606613  26607941      +  26606613
16    1 165696032 165738155      - 165738155
38    1 165696032 165796992      - 165796992
49    1 165865116 165869592      - 165869592
82    1 166026674 166136206      - 166136206
149   1 166244866 166246834      - 166246834

epigenomix documentation built on Nov. 8, 2020, 5:24 p.m.