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Transform VCF Table for QTLseqR

Source: R/pickers.R
picker2.Rd

Function to set comparisons between two samples and output the table in a way that the QTLseq package can use. Uses two element of a list to create a table that can be used by the package QTLseq.

Usage

picker2(df, sample_col = "sample", bulk_col = "bulk")

Arguments

df

A dataframe representing samples vcf_to_qtlseqr_table joined with the sample metadata AND filtered so that only the samples to be compared are present. Note that the levels of the column bulk must be greater than 1

sample_col

name of the column with the sample names. Must contain the low_bulk_sample and high_bulk_sample. Default 'sample'.

bulk_col

name of the column which stores the different sample comparisons. bulk is a name retained from QTLSeqR and traditional BSA experiments

Value

a data.frame with the format that can be understood by QTLseq.

Details

This will be in the format used by QTLseq package. Picker2 has some adaptations from picker 1 for the tabler function in awk. RealDepth instead of realDepth, and no Alt2 allele.