ExpressedGeneInTissue: Returns the id (rownames) of the genes that are found in the...

In barzine/barzinePhdR: Code developed while and for my PhD thesis at the EMBL-EBI

Returns the id (rownames) of the genes that are found in the tissues that have a breadth of expression equals to or lesser than a given one

Description

Returns the id (rownames) of the genes that are found in the tissues that have a breadth of expression equals to or lesser than a given one

Usage

ExpressedGeneInTissue(DFa, nbMax = 2, type = "lim",
  naCol = "nb.tissues", comp = FALSE, threshold, omit.zero)

Arguments

DFa	data.frame; should be logical can be numeric if comp is TRUE
nbMax	integer; breadth of expression maximal to consider
type	character string. "lim" (default) up to the given number as nbMax, "eq" for the exact breadth given by nbMax
naCol	character string. Name of the column which gives the breadth of expression of each gene default: "nb.tissues"
comp	logical; should the breadth of expression be computed first from a numeric DFa
threshold	numeric, which cutoff of expression has to be used for considering a gene expressed in a tissue or not
omit.zero	logical; whether the rows with zeros only should be kept or not

Value

a list that comprises for each column of the inputted data.frame, a vector with the rownames of the genes expressed in a maximal number of tissues (given).

barzine/barzinePhdR documentation built on Nov. 23, 2024, 8:54 p.m.