readXCI {XCIR} | R Documentation |
Read a list of gene symbols of known inactivated genes
to be used as training set in betaBinomXI
.
readXCI(xciGenes = NULL)
xciGenes |
A |
Both gene lists are extracted from Cotton et al. Genome Biology (2013). doi:10.1186/gb-2013-14-11-r122. By default, the function returns a list that was used as training set in the paper. This training set was generated as the intersection of the silenced genes identified by both expression (Carrel & Willard, 2005) and DNA methylation analysis (Cotton et al, 2011). Setting it to "cotton" will instead return a list of 294 genes that were classified as inactivated by Cotton et al. "intersect" is the most stringent list which returns the intersection of training and predicted set.
A character
vector of gene names.
betaBinomXI
xcig <- readXCI() xcig <- readXCI("cotton")