enrichMatrix: Extract chosen enrichment values to a matrix.
In BioinfoHR/coRdon: Codon Usage Analysis and Prediction of Gene Expressivity

Description Usage Arguments Value Examples

Extract enrichment values from multiple samples, i.e. AnnotatedDataFrame objects. Note that the samples should contain annotations of the same type (i.e. the same ontology). The data in matrix format can be easily used in different types of downstream analyses, such as GAGE, and visualised, e.g. using a heatmap.

enrichMatrix(x, variable, replace.na = TRUE)

## S4 method for signature 'list'
enrichMatrix(x, variable, replace.na = TRUE)

`x`	A named list of `AnnotatedDataFrame` objects.
`variable`	Character, indicating the statistic values to extract from `AnnotatedDataFrame` objects in x, must be one of `c("enrich","M","A")`.
`replace.na`	logical, whether to replace NA values in the output. If 'TRUE' (default), NAs will be replaced by 0. Alternatively, if numueric, NAs will be replaced by that given value.

matrix with sequences' annotations as rows, and variable values for different samples as columns.

require(Biobase)

# create contingency table
s <- getKO(LD94)
v <- as.numeric(MELP(LD94, ribosomal = TRUE))
ct <- crossTab(s, v, percentiles = 0.2)

# enrichment analysis
enr <- enrichment(ct)
enr # for help, see `?Biobase::AnnotatedDataFrame`
head(pData(enr$top_0.2), 10)
head(pData(enr$gt_1), 10)
enrm <- enrichMatrix(enr, "M")
head(enrm)