addSNPsToAlnDF: Add SNPs and indels to an alignment data frame

In wrightrc/r1001genomes: Access and analyze the 1001 genomes Arabidopsis resequencing dataset

Description

Add SNPs and indels to an alignment data frame

Usage

addSNPsToAlnDF(aln_df, SNPs, seq_name = Transcript_ID,
  seq_pos = Codon_Number, effect = Effect,
  variant = Amino_Acid_Change, effect_order = SNPeff_order)

Arguments

aln_df	an alignment data frame resulting from makeAlnDF
SNPs	a data frame of SNPs as returned from getCodingDiv
effect_order	a data.frame containing an integer vector named 'strength' representing the strength of the effect, paired with a character vector named 'effect' of possible effects. This will be used to order single and multiple effects.
by_aln_SNPs	a named list of character objects with each equivalency representing matching columns in 'aln_df' (on the LHS) and 'SNPs' (on the RHS), e.g. '"seq_name" = "transcript_id"'

Value

aln_df with the addition of a 'variants' column containing a string listing the variant types at each position

Examples

# make an alignment
IDs <- c("AT3G62980.1", "AT3G26810.1")
alignment <- alignCDS(IDs)
# make an alignment data frame
aln_df <- makeAlnDF(alignment[[2]])
# load a VCF list
vcf <- readRDS(file = system.file("shiny-app", "demo_VCFs.rds",
   package = "r1001genomes"))
vcf <- plyr::ldply(.data = vcf, .fun = subset,
  !is.na(Transcript_ID) & gt_GT != "0|0")
coding_vcf <- getCodingDiv(vcf)
addSNPsToAlnDF(aln_df = aln_df, SNPs = coding_vcf, seq_name = Transcript_ID,
seq_pos = Codon_Number)

wrightrc/r1001genomes documentation built on Nov. 10, 2019, 12:45 p.m.