readXCI: Read a list of known inactivated genes
In SRenan/XCIR: XCI-inference

Description Usage Arguments Details Value See Also Examples

Read a list of gene symbols of known inactivated genes to be used as training set in betaBinomXI.

1	readXCI(xciGenes = NULL)

xciGenes

A character or codeNULL. By defaults, return a vector of 177 genes. Other available choices include "cotton" and "intersect". If a file path is given, the genes will be read from the file.

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