enrichMatrix {coRdon} | R Documentation |
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 |
variable |
Character, indicating the statistic values to extract from
|
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)