chunkAnnotation: Add a chunks column to an annotation data frame

Description Usage Arguments Value Examples

View source: R/VCF_Utils.R

Description

This function adds chunk information for wrapping an alignment and annotations across multiple rows. This will also split individual annotations across rows.

Usage

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chunkAnnotation(anno_df, chunks)

Arguments

anno_df

an annotation data frame from readAnnotationFile with attached alignment positions from addAlnPosToAnno

chunks

a data frame of chunks to facet an alignment/annotation data frame across

Value

anno_df with the addition of chunks columns (and potentially extra rows) for facetting

Examples

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## first make a gene info DF
geneInfo <- getGeneInfo(genes = c("AT3G62980", "AT3G26810"))

## read in an annotation DF
anno_df <- readAnnotationFile(filename = system.file("extdata",
"AFB_annotations.csv", package = "r1001genomes"), gene_info = geneInfo )

## make an alignment DF
IDs <- c("AT3G62980.1", "AT3G26810.1")
alignment <- alignCDS(IDs)
aln_df <- makeAlnDF(alignment[[2]])
aln_df <- chunkAlnDF(aln_df)
chunks <- makeChunksDF(aln_df)

anno_df <- addAlnPosToAnno(anno_df, aln_df)

chunkAnnotation(anno_df, chunks)

wrightrc/r1001genomes documentation built on Nov. 20, 2018, 1:22 a.m.