error.correction: Estimate sequencing errors and compute corrected counts

Description Usage Arguments Author(s) References See Also Examples

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

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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

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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 May 6, 2019, 3:58 a.m.