Package: pumadata 2.48.0

Xuejun liu

pumadata: Various data sets for use with the puma package

This is a simple data package including various data sets derived from the estrogen data for use with the puma (Propagating Uncertainty in Microarray Analysis) package.

Authors:Richard Pearson

pumadata_2.48.0.tar.gz
pumadata_2.48.0.tar.gz(r-4.7-any)pumadata_2.48.0.tar.gz(r-4.6-any)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
pumadata/json (API)

# Install 'pumadata' in R:

install.packages('pumadata', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

affybatch.estrogen - The data from the estrogen package as an AffyBatch object
eset_estrogen_comb - The data from the estrogen package processed using the multi-mgMOS and PUMAcomb algorithms
eset_estrogen_mmgmos - The data from the estrogen package processed using the multi-mgMOS algorithm
eset_estrogen_pmmmgmos - The data from the estrogen package processed using the multi-mgMOS use PM intensities only
eset_estrogen_rma - The data from the estrogen package processed using the RMA algorithm
HTA_Location - The coordinates of probes and the mapped PM probes for hta2.0 chips
HTA_probes_transcripts - The number of probes and the number of transcripts mapped to each gene for hta2.0 chips
HTA_transcript_name - The names of transcripts mapped to each gene for hta2.0 chips
HTA_transcript_NO - The coordinates of probes and the mapped transcripts for hta2.0 chips
Human_Location - The coordinates of probes and the mapped PM for human exon chips
Human_probes_transcripts - The number of probes and the number of transcripts mapped to each gene for human exon chips
Human_transcript_name - The names of transcripts mapped to each gene for human exon chips
Human_transcript_NO - The coordinates of probes and the mapped transcripts for human exon chips
Mouse_Location - The coordinates of probes and the mapped PM for Mouse exon chips
Mouse_probes_transcripts - The number of probes and the number of transcripts mapped to each gene for mouse exon chips
Mouse_transcript_name - The names of transcripts mapped to each gene for mouse exon chips
Mouse_transcript_NO - The coordinates of probes and the mapped transcripts mapped for mouse exon chips
oligo.estrogen - The data from the estrogen package as an ExpressionFeatureSet object
pumapca_estrogen - The data from the estrogen package processed using the pumaPCA algorithm
Rat_Location - The coordinates of probes and the mapped PM for Rat exon chips
Rat_probes_transcripts - The number of probes and the number of transcripts mapped to each gene for rat exon chips
Rat_transcript_name - The names of transcripts mapped to each gene for rat exon chips
Rat_transcript_NO - The coordinates of probes and the mapped transcripts for rat exon chips

On BioConductor:pumadata-2.49.0(data/experiment 3.24)pumadata-2.48.0(data/experiment 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

experimentdata microarraydata snpdata datapkg

4.00 score 6 scripts 0 exports 47 dependencies

Last updated from:5237e70072 (on RELEASE_3_23). Checks:1 ERROR, 2 NOTE, 1 OK. Indexed: no.

This is a data package. Data packages may be large and do not get checked across all platforms.

Target	Result	Time
bioc-checks	ERROR	158
linux-devel	NOTE	322
source / vignettes	OK	599
linux-release	NOTE	324

Exports:

Dependencies:abind affxparser affy affyio Biobase BiocGenerics BiocManager Biostrings bit bit64 blob cachem cli codetools cpp11 crayon DBI DelayedArray fastmap ff foreach generics GenomicRanges glue IRanges iterators lattice lifecycle Matrix MatrixGenerics matrixStats mclust memoise oligo oligoClasses pkgconfig preprocessCore puma rlang RSQLite S4Arrays S4Vectors Seqinfo SparseArray SummarizedExperiment vctrs XVector

pumadata User Guide

Introduction

Rendered frompumadata.Rnwusingutils::Sweave

Last update: 2020-09-07
Started: 2019-09-05

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
The data from the estrogen package as an AffyBatch object	affybatch.estrogen
The data from the estrogen package processed using the multi-mgMOS and PUMAcomb algorithms	eset_estrogen_comb
The data from the estrogen package processed using the multi-mgMOS algorithm	eset_estrogen_mmgmos
The data from the estrogen package processed using the multi-mgMOS use PM intensities only	eset_estrogen_pmmmgmos
The data from the estrogen package processed using the RMA algorithm	eset_estrogen_rma
The coordinates of probes and the mapped PM probes for hta2.0 chips	HTA_Location
The number of probes and the number of transcripts mapped to each gene for hta2.0 chips	HTA_probes_transcripts
The names of transcripts mapped to each gene for hta2.0 chips	HTA_transcript_name
The coordinates of probes and the mapped transcripts for hta2.0 chips	HTA_transcript_NO
The coordinates of probes and the mapped PM for human exon chips	Human_Location
The number of probes and the number of transcripts mapped to each gene for human exon chips	Human_probes_transcripts
The names of transcripts mapped to each gene for human exon chips	Human_transcript_name
The coordinates of probes and the mapped transcripts for human exon chips	Human_transcript_NO
The coordinates of probes and the mapped PM for Mouse exon chips	Mouse_Location
The number of probes and the number of transcripts mapped to each gene for mouse exon chips	Mouse_probes_transcripts
The names of transcripts mapped to each gene for mouse exon chips	Mouse_transcript_name
The coordinates of probes and the mapped transcripts mapped for mouse exon chips	Mouse_transcript_NO
The data from the estrogen package as an ExpressionFeatureSet object	oligo.estrogen
The data from the estrogen package processed using the pumaPCA algorithm	pumapca_estrogen
The coordinates of probes and the mapped PM for Rat exon chips	Rat_Location
The number of probes and the number of transcripts mapped to each gene for rat exon chips	Rat_probes_transcripts
The names of transcripts mapped to each gene for rat exon chips	Rat_transcript_name
The coordinates of probes and the mapped transcripts for rat exon chips	Rat_transcript_NO