importFromTable: Import SNP data from a delimited file

In bmansfeld/QTLseqR: QTL mapping using Bulk Segregant Analysis of Next Generation Sequencing data.

Description

After importing the data from a delimited file, the function then calculates total reference allele frequency for both bulks together, the delta SNP index (i.e. SNP index of the low bulk subtracted from the SNP index of the high bulk), the G statistic and returns a data frame. The required columns in the file are CHROM (Chromosome) and POS (Position) as well as the reference and alternate allele depths (number of reads supporting each allele). The allele depths should be in columns named in this format: AD_(<ALT/REF>).<sampleName>. For example, the column for alternate allele depth for a high bulk sample named "sample1", should be "AD_ALT.sample1". Any other columns describing the SNPs are allowed, ie the actual allele calls, or a quality score. If the column is Bulk specific, It should be named columnName.sampleName, i.e "QUAL.sample1".

Usage

importFromTable(file, highBulk = "HIGH", lowBulk = "LOW",
  chromList = NULL, sep = ",")

Arguments

file	The name of the file which the data are to be read from.
highBulk	The sample name of the High Bulk. Defaults to "HIGH"
lowBulk	The sample name of the Low Bulk. Defaults to "LOW"
chromList	a string vector of the chromosomes to be used in the analysis. Useful for filtering out unwanted contigs etc.
sep	the field separator character. Values on each line of the file are separated by this character. Default is for csv file ie ",".

Value

Returns a data frame containing columns for per bulk total Read depth (DP), Reference Allele Depth (AD_REF) and Alternative Allele Depth (AD_ALT), any other SNP associated columns in the file, and SNPindex for each bulk (indicated by .HIGH and .LOW column name suffix). Total reference allele frequnce "REF_FRQ" is the sum of AD_REF for both bulks divided by total Depth for that SNP. The deltaSNPindex is equal to SNPindex.HIGH - SNPindex.LOW.

bmansfeld/QTLseqR documentation built on Jan. 25, 2020, 8:52 p.m.