mergeSeq: Merge sequences

In fmichonneau/chopper: Alignment Manipulations and Data Preparation for Phylogenetic Analyses

Description

Creates a set of alignments for given a list of extractions and markers.

Usage

mergeSeq(listFiles, output, seqFolder = "~/Documents/seqRepository",
  markers = c("16S", "16Sc"), checkAmbiguity = TRUE, gblocks = NULL,
  gapchar = "?", justCheck = FALSE)

Arguments

listFiles	names (vector of character) of the individual sequence files to be merged.
output	folder where the write the output files. If the folder doesn't exist, the user is asked whether it should be created.
seqFolder	the folder that contains the individual files being stored in their own folders.
markers	the list of markers to be used to build the alignemnt. They need to match the subfolders found in ‘seqFolder’
checkAmbiguity	Should the sequences be checked for ambiguities before merging?
gblocks	If different from NULL, gblocks should be a named list with the marker as its names and the parameters to be passed to Gblocks as its values. This function assumes that the extension of the file created by Gblocks is ‘-gb’ so you don't want to use the ‘-e=’ flag.
gapchar	Characters to be used to create empty sequences for files that are not sequenced for a given marker.
justCheck	If FALSE, no alignment is created.

Details

This function takes a list of extractions and creates alignments from them. When more than one marker is specified, empty sequences might be added if they are not available for this particular marker, to create alignments with the same number of sequences across all markers. The alignment is being performed by MUSCLE. This function can also call Gblocks to remove ambiguous parts in the alignment. To function properly R needs to be able to access MUSCLE and Gblocks with the command system(), this means that the executables need to be in your PATH.

Value

Mostly used for its side effect of creating alignment for a list of extractions, given a list of markers. Invisibly returns a data frame that includes which extraction has been sequenced for which marker, with as attributes the file names created.

Author(s)

Francois Michonneau

fmichonneau/chopper documentation built on May 16, 2019, 1:43 p.m.