make.readsets: Automatically load readsets by grouping .ab1 files by name.

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

Description

Automatically load readsets by grouping .ab1 files by name.

Usage

make.readsets(input.folder, forward.suffix, reverse.suffix, trim = TRUE,
  trim.cutoff = 1e-04, processors = NULL, min.length = 1,
  max.secondary.peaks = NULL, secondary.peak.ratio = 0.33)

Arguments

input.folder	The parent folder of all of the reads contained in ab1 files you wish to analyse. Subfolders will be scanned recursively.
forward.suffix	the suffix of the filenames for forward reads, i.e. reads that do not need to be reverse-complemented. Include the full suffix, e.g. "forward.ab1".
reverse.suffix	the suffix of the filenames for reverse reads, i.e. reads that *do* need to be reverse-complemented. Include the full suffix, e.g. "reverse.ab1".
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
processors	The number of processors to use, or NULL (the default) for all available processors
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.
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.

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