GenoView (version 1.6.0)

makeGR: Make GRanges object from data.frame

Description

Extracts GRanges data from relevant columns from a data.frame, performs seqlengths adjustments and complete case filtering

Usage

makeGR(dataFrame, chr.col, s.p.col, e.p.col, str.col, 
id.col = NULL, plot.int, des.seqs, show.legend = FALSE, l.height = 0)

Arguments

dataFrame

Data.frame which contains at least Chromosome, Start Position, End Position, and Strand data. It may also contain a column which uniquely identifies each entry for legend plotting.

chr.col

Chromosome data column name

s.p.col

Start position data column name

e.p.col

End position data column name

str.col

Strand data column name

id.col

Fill data column name

plot.int

GRanges object of length 1 of the plotting interval in genomic coordinates

des.seqs

Desired seqlengths appropriate for dataFrame

show.legend

Determines whether legend information is kept based on boolean

l.height

Determines whether legend information is kept based on height allocation

Value

GRanges object containing filtered genomic data

Examples

library(biovizBase)

# Create a missense mutations dataset in TP53
set.seed(1)
N = 25
locations = sample(7571720:7590863, size = N)
mut.df <- data.frame(chrom = "chr17", 
                    start = locations, 
                    end = locations, 
                    str = "-", 
                    fill = 1:N)

# Create a truncated plotting interval
plot.int = GRanges(seqnames = "chr17", 
                    IRanges(start = 7576000, end = 7579000), 
                    strand = "-")

# Obtain hg19 seqlengths data
data(hg19Ideogram, package = "biovizBase")
seqs.hg19 <- seqlengths(hg19Ideogram)

makeGR(dataFrame = mut.df, chr.col = "chrom", s.p.col = "start", 
        e.p.col = "end", str.col = "str", id.col = "fill", 
        plot.int = plot.int, show.legend = TRUE, 
        des.seqs = seqs.hg19)