overlapSpeProtmRNA: Overlap of the tissue-specific proteins with the most...
In barzine/barzinePhdR: Code developed while and for my PhD thesis at the EMBL-EBI

overlapSpeProtmRNA

R Documentation

Overlap of the tissue-specific proteins with the most specific transcripts to that tissue.

Description

Overlap of the tissue-specific proteins with the most specific transcripts to that tissue.

Usage

overlapSpeProtmRNA(DFprot, DFmRNA, pretreatment = FALSE,
  mRNAmethod = "ratioSpe", cutoffProt = 0, complete.matrix = TRUE,
  pvalue = TRUE, ratio = 1, xprot = NA, yrna = NA, figure = TRUE,
  ...)

Arguments

`DFprot`	numeric data.frame of the protein expression data
`DFmRNA`	numeric data.frame of the transcriptomic expression data
`pretreatment`	boolean. Default: FALSE. Whether the considered tissues (columns) and genes (rows) need to be filtered to the common set. The function requires the same set of tissues/genes to be meaningful. This step can be bypassed if it already happened previously.
`mRNAmethod`	a function name. The function should allow to order the mRNAs based on their specificity rank.
`cutoffProt`	numeric. Threshold to consider a protein is expressed.
`complete.matrix`	boolean. Default:TRUE. Whether the comparison between the two studies should be done for their whole data.frame
`pvalue`	boolean. Default: TRUE. Whether the p-value of the jaccard index should be computed
`ratio`	numeric (>0). Multiplying factor that allows increasing the number of transcripts compared with the proteins.
`xprot`	character string. Default: NA. Needed when complete.matrix is false. Name of the tissue to consider for the proteomics.
`yrna`	character string. Default: NA. Needed when complete.matrix is false. Name of the tissue to consider for the transcriptomics.
`figure`	boolean. Default: TRUE. Whether the venn diagram should be drawn
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