intePareto v0.0.1

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by Yingying Cao View Source

Integrative Analysis of RNA-Seq and ChIP-Seq Data

Integrative analysis of gene expression (RNA-Seq data), and histone modification data for user-defined sets of histone marks (ChIP-Seq data) to discover consistent changes in genes between biological conditions. Additionally, Pareto optimization is used to prioritize genes based on the level of consistent changes in both RNA-Seq and ChIP-Seq data.

Functions in intePareto

Name	Description
df_final	an example of the result of doIntegration
test_rna_meta	meta data of preprocessed RNA-Seq data
promoter	an example of promoter region
res	an example of the result of doMatch
counts2lFC	Calculate log2FoldChange
bam2rpm	Compute the normalized number of reads (rpm) fall into specific genomic region
doIntegration	Do integrative analysis
test_chip_meta	meta data of preprocessed ChIP-Seq data
bam2counts	Compute the number of reads fall into specific genomic region
doPareto	Prioritization of genes based on Z scores
doMatch	Match the RNA-Seq and ChIP-Seq data on the gene level
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Vignettes of intePareto

Name
intePareto.Rmd
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Details

Type	Package
Date	2019-10-08
License	GPL (>= 2)
LazyLoad	yes
NeedsCompilation	no
ByteCompile	true
Encoding	UTF-8
Packaged	2019-10-08 18:20:45 UTC; yingying
RoxygenNote	6.1.1
VignetteBuilder	knitr
Repository	CRAN
Date/Publication	2019-10-09 16:10:02 UTC

imports	apeglm , biomaRt , DESeq2 , GenomeInfoDb , GenomicAlignments , GenomicRanges , IRanges , rPref , Rsamtools
suggests	knitr , rmarkdown
depends	R (>= 3.6.0)
Contributors