sagenhaft (version 1.42.0)

sage.utilities: Utilities

Description

Different utilities to use with SAGE data.

Usage

tagnum2tagmatrix(tags, length)
tagmatrix2tagnum(tags, length=ncol(tags))
tagnum2tagsequence(tags, length)
tagsequence2tagnum(tags, length)
revcomp(seq)

Arguments

tags

integer or character vector giving SAGE tags.

length

Length of SAGE tags.

seq

Character vector or list of sequences.

...

SAGE library objects.

Details

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.

Examples

library(sagenhaft)
tags <- c("aaa", "ttt", "ccc")
tagsnumeric <- tagsequence2tagnum(tags, 3)
tagsmatrix <- tagnum2tagmatrix(tagsnumeric, 3)
tags <- tagnum2tagsequence(tagmatrix2tagnum(tagsmatrix, 3), 3)
revcomp(tags)