error.correction: Estimate sequencing errors and compute corrected counts

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

Description

These functions are used to compute sequencing error correction in a library. They are automatically called when extracting tags from sequences and therefore usually do not have to be called directly.

Usage

estimate.errors.mean(lib)
compute.sequence.neighbors(tags, taglength=10, quality.scores=NULL,
                           output="character") 
em.estimate.error.given(lib, maxstep=50, ...)

Arguments

lib	A sage library object
tags	A character vector or numeric vector containing tags
taglength	length of tag
quality.scores	A matrix containing base quality scores as -10 log10 Pe
maxstep	iterations of EM algorithm
output	Output type for compute.sequence.neighbors, either character or numeric
...	Other arguments ignored.

Author(s)

Tim Beissbarth

References

http://tagcalling.mbgproject.org

See Also

extract.lib, sage.library

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")) 
testlib <- combine.libs(B6Hypo, E15post)
testlib <- estimate.errors.mean(testlib)
testlib <- em.estimate.error.given(testlib)
tagneighbors <- compute.sequence.neighbors(testlib$seqs[,"seq"], 10,
                          testlib$seqs[,paste("q", 1:10, sep="")]) 

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