sage.library.comparison: Class sage.library.comparison

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

Description

Class for storing the data of a pairwise comparison between two SAGE libraries.

Usage

read.sage.library.comparison(file)
write.sage.library.comparison(x, file=paste(x$name, "sagecomp", sep="."))
compare.lib.pair(lib1, lib2) 

Arguments

x,lib1,lib2	A sage library object
file	File name to read or write to

Details

SAGE library comparison objects consists of one data.frames. It stores a A and an M value which are the log2 average expression and log2 ratio, respectively. It also has a column for the resulting p.values from sage.test. read.sage.library.comparison and write.sage.library.comparison are utility functions to read and write SAGE library comparisons. compare.lib.pair can be used to generate SAGE library comparisons.

Author(s)

Tim Beissbarth

References

http://tagcalling.mbgproject.org

See Also

sage.test

Examples

library(sagenhaft)
B6Hypo <- read.sage.library(system.file("extdata", "B6HypothalHFI.sage",
                            package="sagenhaft")) 
E15post <- read.sage.library(system.file("extdata","E15postHFI.sage",
                             package="sagenhaft")) 
libcomp <- compare.lib.pair(B6Hypo, E15post)
plot(libcomp)
libcomp

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