subsetGenes: Subet Genes or Variables from a Dataset

In axm323/dataVisEasy: datavisEasy: Data visualizations Using Annotations Made Easy

Subet Genes or Variables from a Dataset

Description

Quick function to subset genes/variables from a data matrix based on an annotation or characteristic. Can also pull out genes/variables by name with the option to order the columns by expression of a given gene.

Usage

subsetGenes(data, group, take.out, list, order.by = NULL, exact = F,
subset.by = "annotation")

Arguments

data	numeric data matrix with samples/observations in the columns and genes/variables in the rows
group	character string pointing to a column name in the annotations.genes stored in params. Can also supply a custom vector the same length as the rows of the input matrix.
take.out	level or levels of the group vector supplied indicating the genes to be extracted
list	character vector of genes/variables to be pulled out of the data matrix for viewing
order.by	optional string equal to one of the rownames of the supplied data frame. Columns of output data matrix will be ordered according to the supplied gene from lowest to highest expression value.
exact	whether or not to search for exact or inexact matches of 'list' in 'data'. If exact = T (default) output will contain genes/variables that exactly match the list supplied. If set to FALSE, will search for inexact matches.
subset.by	whether to subset by an annotation stored in params$annotations.genes ("annotation", default) or by the a list of names to search for in row names ("name")

Value

data matrix with the same number of columns as the input data matrix but subset for the specified gene/variable list

Author(s)

~~Alison Moss~~

Examples

ion.subset <- subsetGenes(RAGP_norm, list = c("Kcn","Cacn","Hcn","Scn"),
exact = FALSE, subset.by = "name")

axm323/dataVisEasy documentation built on Feb. 1, 2024, 11:53 p.m.