readData: Read alignments and calculate summary data

In pievos101/PopGenome: An Efficient Swiss Army Knife for Population Genomic Analyses

Read alignments and calculate summary data

Description

This function reads alignments/SNP data in several formats and calculates some summary data.

Usage

readData(path,populations=FALSE,outgroup=FALSE,include.unknown=FALSE,
         gffpath=FALSE,format="fasta",parallized=FALSE,
         progress_bar_switch=TRUE, FAST=FALSE,big.data=FALSE,
         SNP.DATA=FALSE
        )

## S4 method for signature 'GENOME'
get.sum.data(object)

Arguments

object	object of class "GENOME"
path	the basepath (folder) of the alignments
outgroup	vector of outgroup sequences
include.unknown	if positions with unknown nucleotides should be considered.
populations	list of populations. default:FALSE
gffpath	the basepath (folder) of the corresponding GFF-files. default:FALSE
format	data formats. "fasta" is default. See details !
parallized	parallel processing to accelerate the reading process. See details !
progress_bar_switch	progress_bar
FAST	fast computation. See details !
big.data	use the ff-package
SNP.DATA	important for reference positions; should be TRUE if you use SNP-data in alignment format

Details

All data (alignments or SNP-files) have to be stored in one folder. The folder is the input of this
function. If no GFF file (which also have to be stored in a folder) is specified, an alignment in
the correct reading frame (starting at a first codon position) is expected.
Otherwise synonymous and non-synonymous positions are not identified correctly.

Note:
The GFF-files have to be EXACTLY the same names (without any extensions like .fas or .gff)
as the files storing the nucleotide data to ensure correct matching

format:
"fasta","nexus","phylip",
"MAF","MEGA"
"HapMap","VCF"
"RData"
Valid nucleotides are T,t,U,u,G,g,A,a,C,c,N,n,-

parallized:
- will speed up calculations if you use a very large amount of alignments

FAST:
- will not classify synonymous/non-synonymous SNPs directly
- fast computation (via compiled C code) of biallelic matrix, biallelic sites, transversions/transitions
and biallelic substitutions
- can be switched to TRUE in case of SNP data without loss of information

big.data:
- use the ff-package
- ff mechanism is used for biallelic.matrix and GFF/GTF information
- is automatically activated for readVCF or readSNP
- Note! you should set this to TRUE if you use big chunks of data
and you want to later concatenate them in the PopGenome framework
(for example: sliding windows of the whole dataset).

SNP.DATA:
- should be switched to TRUE if you use SNP-data in alignment format.
- the corresponding SNP positions can be set via set.ref.positions

Value

The function creates an object of class "GENOME"

———————————————————
The following slots will be filled in the "GENOME" object
———————————————————

	Slot	Description
1.	n.sites	total number of sites
2.	n.biallelic.sites	number of biallelic sites
3.	n.gaps	number of sites with gaps
4.	n.unknowns	number of sites with unknown nucleotides
5.	n.valid.sites	number of valid sites
6.	n.polyallelic.sites	number of sites with >2 nucleotides
7.	trans.transv.ratio	transition/transversion ratio of biallelic sites
8.	region.names	names of regions
9.	region.data	some detailed information about the data read

Examples

# GENOME.class <- readData("...\Alignments", FAST=TRUE)
# GENOME.class <- readData("VCF", format="VCF")
# Note, "Alignments" and "VCF" are folders !
# [e-mail]
# GENOME.class <- readData("...\Alignments", big.data=TRUE)
# object.size(GENOME.class)
# GENOME.class <- readData("...\Alignments",gffpath="...\Alignments_GFF")
# GENOME.class
# show the result:
# get.sum.data(GENOME.class)
# [e-mail]

pievos101/PopGenome documentation built on May 23, 2024, 7:31 p.m.