sage.utilities: Utilities

In sagenhaft: Collection of functions for reading and comparing SAGE libraries

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.

Author(s)

Tim Beissbarth

Examples

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

sagenhaft documentation built on Nov. 8, 2020, 4:57 p.m.