getQTLTable: Export a summarized table of QTL

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

Description

Export a summarized table of QTL

Usage

getQTLTable(SNPset, method = "Gprime", alpha = 0.05, interval = 99,
  export = FALSE, fileName = "QTL.csv")

Arguments

SNPset	Data frame SNP set containing previously filtered SNPs
method	either "Gprime" or "QTLseq". The method for detecting significant regions.
alpha	numeric. The required false discovery rate alpha for use with method = "Gprime"
interval	numeric. For use eith method = "QTLseq" The Takagi based confidence interval requested. This will find the column named "CI_\*\*", where \*\* is the requested interval, i.e. 99.
export	logical. If TRUE will export a csv table.
fileName	either a character string naming a file or a connection open for writing. "" indicates output to the console.

Value

Returns a summarized table of QTL identified. The table contains the following columns:

• id - the QTL identification number

• chromosome - The chromosome on which the region was identified

• start - the start position on that chromosome, i.e. the position of the first SNP that passes the FDR threshold

• end - the end position

• length - the length in basepairs from start to end of the region

• nSNPs - the number of SNPs in the region

• avgSNPs_Mb - the average number of SNPs/Mb within that region

• peakDeltaSNP - the tricube-smoothed deltaSNP-index value at the peak summit

• posPeakDeltaSNP - the position of the absolute maximum tricube-smoothed deltaSNP-index

• maxGprime - the max G' score in the region

• posMaxGprime - the genomic position of the maximum G' value in the QTL

• meanGprime - the average G' score of that region

• sdGprime - the standard deviation of G' within the region

• AUCaT - the Area Under the Curve but above the Threshold line, an indicator of how significant or wide the peak is

• meanPval - the average p-value in the region

• meanQval - the average adjusted p-value in the region

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