correlationRpkmCopyNo: Generates a data.frame of the Genes' names, copy numbers, and...
In asishallab/GeneFamilies: Analyses different properties of gene families

correlationRpkmCopyNo

R Documentation

Generates a data.frame of the Genes' names, copy numbers, and expression values (RPKM). Furthermore, computes a lm model for the observed data. If expression levels are extracted for more than a single tissue the `mean` value is used. Note, that only genes are considered that have some expression in any tissue, never expressed genes are discarded from the analysis.

Description

Generates a data.frame of the Genes' names, copy numbers, and expression values (RPKM). Furthermore, computes a lm model for the observed data. If expression levels are extracted for more than a single tissue the mean value is used. Note, that only genes are considered that have some expression in any tissue, never expressed genes are discarded from the analysis.

Usage

correlationRpkmCopyNo(rpkm.df = rpkm.rna.seq.counts, r.gene.col = "id",
  r.rpkm.col = "expression", r.tissue.col = "tissue",
  copy.no.df = gene.copy.number.df, c.gene.col = "Gene.no.expr.var",
  c.copy.no.col = "copy.no", tissues = unique(rpkm.df[, r.tissue.col]),
  stat.funk = mean, lapply.funk = lapply)

Arguments

`rpkm.df`	An instance of data frame holding the genes expression counts (RPKM). Default is `rpkm.rna.seq.counts`.
`r.gene.col`	A string or integer identifying the column of `rpkm.df` in which to find the gene accessions (IDs). Default is `'id'`.
`r.rpkm.col`	A string or integer identifying the column of `rpkm.df` in which to find the genes' expression counts (RPKM). Default is `'expression'`.
`r.tissue.col`	A string or integer identifying the column of `rpkm.df` in which to find the tissue in which the expression was measured. Default is `'tissue'`.
`copy.no.df`	An instance of `base:data.frame` in which to find the genes' copy numbers. Default is `'gene.copy.number.df'`.
`c.gene.col`	A string or integer identifying the column of `copy.no.df` in which the gene accessions (IDs) are stored. Default is `'Gene.no.expr.var'`.
`c.copy.no.col`	A string or integer identifying the column of `copy.no.df` in which the genes' copy numbers are held. Default is `'copy.no'`.
`tissues`	A character of minimum length one in which the tissues to extract expression levels for are stored. Default is `unique(rpkm.df[, r.tissue.col])`
`stat.funk`	The statistical measure applied on the expression values found for a respective gene within the argument `tissues`. Default is `base::mean`.
`lapply.funk`	One of `base::lapply` or `parallel::mclapply` to indicate which function shall be used to iterate over the respective genes. Default is `lapply`.