sage.utilities {sagenhaft} | R Documentation |
Different utilities to use with SAGE data.
tagnum2tagmatrix(tags, length) tagmatrix2tagnum(tags, length=ncol(tags)) tagnum2tagsequence(tags, length) tagsequence2tagnum(tags, length) revcomp(seq)
tags |
integer or character vector giving SAGE tags. |
length |
Length of SAGE tags. |
seq |
Character vector or list of sequences. |
... |
SAGE library objects. |
These functions are utility functions used in SAGE tag extraction, e.g. to convert SAGE tag sequences to numeric values, i.e. base 4 for efficient storage and handling, and to reverse complement sequences.
Tim Beissbarth
library(sagenhaft) tags <- c("aaa", "ttt", "ccc") tagsnumeric <- tagsequence2tagnum(tags, 3) tagsmatrix <- tagnum2tagmatrix(tagsnumeric, 3) tags <- tagnum2tagsequence(tagmatrix2tagnum(tagsmatrix, 3), 3) revcomp(tags)