spViewPerFeature: Tools to visualize genomic data

In ShortRead: FASTQ input and manipulation

Description

Use Snapshot-class to visualize a specific region of genomic data

Usage

spViewPerFeature(GRL, name, files, ignore.strand=FALSE,
                 multi.levels = FALSE, fac=character(0L), ...) 

Arguments

GRL	Object GRangeList containing annotation of genomic data. It can be generated by applying exonsBy() or transcriptsBy() to a TxDb instance. See examples below.
name	Character(1) specifying which element in GRL to be visualized.
files	Charactor() or BamFileList specifying the file(s) to be visualized. If multiple files, local metadata of the files can be hold by setting a DataFrame (values(files) <- DataFrame(...)). See examples below.
ignore.strand	Logical(1) indicating whether to ignore the strand of the genomic data.
multi.levels	Logical(1) indicating whether to plot the coverage of multiple files on different panels. If FALSE, the mean coverage of multiple files would be plotted.
fac	Character(1) indicating which column of local metadata (elementMetatdata()) should be used to group the samples. Ignore
...	Arguments used for creating a Snapshot object.

Value

A Snapshot instance

Author(s)

Chao-Jen Wong [e-mail]

See Also

Snapshot

Examples

## Example 1
library(GenomicFeatures)
txdbFile <- system.file("extdata", "sacCer2_sgdGene.sqlite",
                         package="yeastNagalakshmi")

## either use a txdb file quaried from UCSC or use existing TxDb packages.
txdb <- loadDb(txdbFile)

grl <- exonsBy(txdb, by="gene")
file <- system.file("extdata", "SRR002051.chrI-V.bam",
                         package="yeastNagalakshmi")
s <- spViewPerFeature(GRL=grl, name="YAL001C", files=file)

## Example 2
## multi-files: using 'BamFileList' and setting up the 'DataFrame'
## holding the phenotype data

bfiles <- BamFileList(c(a=file, b=file))
values(bfiles) <- DataFrame(sampleGroup=factor(c("normal", "tumor")))
values(bfiles)

s <- spViewPerFeature(GRL=grl, name="YAL001C",
                      files=bfiles, multi.levels=TRUE, fac="sampleGroup")

ShortRead documentation built on Nov. 8, 2020, 8:02 p.m.