make.readset: Make a readset

In mammerlin/sangeranalyseR: sangeranalyseR: a suite of functions for the analysis of Sanger sequence data in R

Description

Make a readset

Usage

make.readset(fwd.fnames, rev.fnames, trim = TRUE, trim.cutoff = 1e-04,
  max.secondary.peaks = NULL, secondary.peak.ratio = 0.33, min.length = 1,
  processors = NULL)

Arguments

fwd.fnames	a list of full file paths to forward reads from ab1 files (i.e. those that do not need to be reverse-complemented).
rev.fnames	a list of full file paths to reverse reads from ab1 files (i.e. those that *do* need to be reverse-complemented).
trim	TRUE/FALSE trim sequences based on quality while creating readgroup? If TRUE, the trim.mott function is applied to each sequence before inclusion in the readgroup. Note, trimming only works if the raw data are stored in ab1 files with appropriate information.
trim.cutoff	value passed to trim.mott as quality cutoff for sequencing trimming, only used if 'trim' == TRUE
max.secondary.peaks	reads with more secondary peaks than this will not be included in the readset. The default (NULL) is to include all reads regardless of secondary peaks
secondary.peak.ratio	Only applies if max.secondary.peaks is not NULL. The ratio of the height of a secondary peak to a primary peak. Secondary peaks higher than this ratio are counted. Those below the ratio are not.
min.length	reads shorter than this will not be included in the readset. The default (1) means that all reads with length of 1 or more will be included.
processors	The number of processors to use, or NULL (the default) for all available processors

Value

A set of unaligned reads as a DNAstringset object, names are the input file paths. Note that secondary peaks are encoded in these reads as ambiguous bases using IUPAC ambiguity codes.

mammerlin/sangeranalyseR documentation built on May 13, 2019, 1:08 p.m.