Description Usage Arguments Details Value See Also Examples
Hierarchical annotation of the CAGE clusters
hannot(annot, hierarchy = "default")
A character vector of annotations.
Either the character “default”, or a data frame whith patterns in its first column and keywords in its second column. The default data frame is picked when “default” is passed as argument.
The default data frame is as follows (as of version 0.2.1).
None None snoscan other antisense antisense intron,sense\| intron exon,sense\| exon lncRNA\| exon miRNA\| miRNA snRNA\| snRNA snoRNA\| snoRNA tRNA\| tRNA
Parses a vector of annotations in character format an returns a vector of annotations as factors, where one single keyword has been selected from a provided list or the default list (see below).
A vector of annotations as factors, where the levels are sorted in the hierarchical order. For instance, with the data frame above, if an annotation matches for the keywords ‘miRNA’ and ‘snoRNA’, then the reported one will be ‘snoRNA’.
Other smallCAGEqc annotation functions:
1 2 3 4
x <- c('exon,sense|foo', 'foo', 'antisense of bar', 'intron,sense|bar' , 'antisense of baz;snoRNA|SNORA70') hannot(x) cbind(x, as.character(hannot(x)))
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