error.correction {sagenhaft} | R Documentation |
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.
estimate.errors.mean(lib) compute.sequence.neighbors(tags, taglength=10, quality.scores=NULL, output="character") em.estimate.error.given(lib, maxstep=50, ...)
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. |
Tim Beissbarth
http://tagcalling.mbgproject.org
library(sagenhaft) B6Hypo <-read.sage.library(system.file("data/B6HypothalHFI.sage", package="sagenhaft")) E15post <- read.sage.library(system.file("data/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="")])