BreastCancer: Multiple RNA-Seq count data designed as Breast Cancer cell...

In metaSeq: Meta-analysis of RNA-Seq count data in multiple studies

Description

A data frame with 23368 rows (genes) with following 18 columns (samples).

All reads were measured by Illumina Genome Analyzer II or IIX, trimmed as 36 base, and mapped to the human reference genome hg19 as single-end. Each experimental design was restricted as Breast cancer cell vs Normal cell. Quality Control was performed by FastQC and samples whose quality scores were at least over 20 were choosed. Counts are quantified by HTSeq.

Usage

data(BreastCancer)

Details

StudyA: SRP008746

• A_1: Breast Cancer (HCC1937), SRX099961, SRR350976

• A_2: Breast Cancer (HCC3153), SRX101334, SRR353604_1

• A_3: Breast Cancer (SUM131502), SRX101335, SRR353948_1

• A_4: Normal (MCF10A), SRX099963, SRR353603_1

• A_5: Normal (HCC2337), SRX101336, SRR353602_1

StudyB: SRP006726

• B_1: Breast Cancer (HCC1954), SRX061997, SRR201983

• B_2: Normal (HMEC), SRX061998, SRR201986

StudyC: SRP005601

• C_1: Breast Cancer (BT20), SRX040501, SRR097786_1

• C_2: Breast Cancer (BT474), SRX040502, SRR097787_1

• C_3: Breast Cancer (MCF7), SRX040504, SRR097789_1

• C_4: Breast Cancer (MDAMB231), SRX040505, SRR097790_1

• C_5: Breast Cancer (MDAMB468), SRX040506, SRR097791_1

• C_6: Breast Cancer (T47D), SRX040507, SRR097792_1

• C_7: Breast Cancer (ZR751), SRX040508, SRR097793_1

• C_8: Normal (MCF10A), SRX040503, SRR097788_1

StudyD: ERP000992

• D_1: Breast Cancer (MCF7), ERX030989, ERR053953

• D_2: Breast Cancer (T47D), ERX031000, ERR053958

• D_3: Normal (Ishikawa), ERX030994, ERR053948

Source

https://trace.ddbj.nig.ac.jp/DRASearch/study?acc=SRP008746

http://trace.ddbj.nig.ac.jp/DRASearch/study?acc=SRP006726

http://trace.ddbj.nig.ac.jp/DRASearch/study?acc=SRP005601

http://trace.ddbj.nig.ac.jp/DRASearch/study?acc=ERP000992

References

Hon, G. C. and Hawkins, R. D. and Caballero, O. L. and Lo, C et al. (2012) Global DNA hypomethylation coupled to repressive chromatin domain foormation and gene silencing in breast cancer. Genome Research, 22 (2): 246-258

Sun, Z. and Asmann, Y. W. and Kalari, K. R. and Bot, B. et al. (2011) Integrated analysis of gene expression, CpG island methylation, and gene copy number in breast cancer cells by deep sequencing. PLOS ONE, 25;6(2): e17490

See Also

StudyA, pvals.

Examples

data(BreastCancer)

Example output

Loading required package: NOISeq
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: splines
Loading required package: Matrix
Loading required package: snow

Attaching package: 'snow'

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

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, clusterSplit, parApply, parCapply,
    parLapply, parRapply, parSapply

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

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, clusterSplit, makeCluster, parApply,
    parCapply, parLapply, parRapply, parSapply, splitIndices,
    stopCluster

Loading required package: Rcpp

metaSeq documentation built on Nov. 8, 2020, 7:26 p.m.