expressionProfilesDists: Computes the distance ('base::dist') between the expression...

View source: R/expression_funks.R

expressionProfilesDistsR Documentation

Computes the distance (base::dist) between the expression profiles of the genes in argument gene.accessions.

Description

Computes the distance (base::dist) between the expression profiles of the genes in argument gene.accessions.

Usage

expressionProfilesDists(gene.accessions,
  expression.profiles = rna.seq.exp.profils,
  expr.prof.gene.col = "gene",
  expr.prof.gene.variant.col = "gene.exp.var",
  tissues = setdiff(colnames(expression.profiles), c(expr.prof.gene.col,
  expr.prof.gene.variant.col)), dist.method = "euclidean",
  per.tissue = FALSE)

Arguments

gene.accessions

A character vector of gene identifiers some of which are expected to be present in expression.profiles

expression.profiles

A data.frame with gene expression profiles. Default is this package's rna.seq.exp.profils data.

expr.prof.gene.col

A number or string identifying the column of expression.profiles in which to lookup the gene accessions. Default is 'gene'.

expr.prof.gene.variant.col

A number or string identifying the column of expression.profiles in which to lookup the gene accessions including their expression variant identifier (e.g. 'AT1G12345.3'). Default is gene.exp.var.

tissues

A character or integer indexing those columns of expression.profiles in which the actual relative expression per tissue is stored. In short these columns are the expression profiles. Default is setdiff(colnames(expression.profiles), c(expr.prof.gene.col, expr.prof.gene.variant.col)).

dist.method

A string to pass as argument method to base::dist. Default is 'euclidean'.

per.tissue

Logical indicating wether to compute distances in the euclidean space created by the dimensions of all tissues, or if set to TRUE computes the one-dimensional distances per tissue. Default is FALSE.

Value

An instance of base::dist holding pairwise distances between the argument genes expression profiles. If not at least two expression profiles are found for the argument gene.accessions NA is returned. In case the argument per.tissue is set to TRUE a list of one-dimensional distances is returned; names of the list are the respective tissues.


asishallab/GeneFamilies documentation built on May 22, 2023, 11:30 a.m.