annotation {iGenomicViewer}R Documentation

Functions for Creating the Annotation Object

Description

These functions are designed to create an annotation object.

Usage


makeAnnotation(file,
               label,
               chrom,
               chrom.levels,
               band.info=NA,
               loc=NA,
               loc.start=NA,
               loc.stop=NA,
               file.sep="\t",
               additional=NA,
               names.additional = NA,
               links=NA,
               names.links=NA,
               images=NA,
               names.images=NA,
               returnVl = TRUE,
               saveVl = FALSE,
               saveName="Annotation.RData",
               ...)

annotationObj(annotation,  
              annotationObj = NA, 
              obj.name = NA,
              returnVl = TRUE,
              saveVl = FALSE,
              saveName="AnnotationObj.RData")

Arguments

file path name of file
label column in file that represents the label for annotation region
chrom column in file that represents the chromosome location
chrom.levels vector indicating how the chrom column is represented. i.e chr1, chrom1, 1, etc.
band.info a band.info object. see makeBandInfo
loc column in file representing genomic location. See details for more information
loc.start column in file representing starting genomic location. See details for more information
loc.stop column in file representing ending genomic location. See details for more information
file.sep seperation character for file
additional indication of additional columns in file that should be included in annotation object
names.additional optional header names for additional columns to be included
links indication of columns in file that represent hyperlinks, character or numeric, or a data.frame of hyperlinks, with rows equal to the number of rows in the file, and in the same order as they appear in the file
names.links optional header names for links
images indication of columns in file that represent images, character or numeric, or a data.frame, with rows equal to the number of rows of the file, of images that must be in the same order as they appear in the file
names.images optional header names for images
returnVl logical indicating if object created should be returned
saveVl logical indicating if object created should be saved to a file
saveName if saveVl, path name of file
annotation annotation object created by the makeAnnotation function
annotationObj annotation object created by annotationObj function. If NA, creates a new object.
obj.name name of the annotation set in the annotationObj
... additional arguments to the read.table function for reading the file

Details

The annotationObj is a larger object that contains all individual annotation information desired for a genomic mapping. These annotations will be represented in a track along side of the main heatmap of the iGGV function. Each individual annotation information object must be added separatly to the main annotationObj.

The annotation file must minimally contain columns for name, chromosome, and genomic location. The genomic location may be given by a single value assumed to be a central location and should be specified using the loc argument. This value should be the genomic location with respect to the entire genome not the location within a chromosome. The other, recommended, way of specifing the genomic location is with both a starting and stopping genomic location, and should be specified using loc.start and loc.stop arguments. These values are the location within the chromosome not over the entire genome. If loc.start and loc.stop are used, loc should be NA.

The band.info argument is an object of the class band.info. This object contains information about chromosome, arm, broad.band, and fine.band regions. See band.info help files for details.

The iGGV function has the capabilities of including hyperlinks in displayed tool-tips. In order for the links to display properly they need to be specified in the annotation object. If there are links in the file, the column number or head name may be specified as links. The user may add their own hyperlinks by assigning the links argument to a table of the dimension n by m where n is equivalent to the number of items in the original file. The links must be in proper format of a valid web address, i.e http://completewebpathhere.com . Similarly, images may also be displayed and set through the images argument.

Value

annotationObj returns an object containing annotation information objects.
makeAnnotation returns an object of the class anninfo. This object contains annotation information such as labels, chromosome locations, genomic locations, and web links.

Note

For an example object see annObj

Author(s)

Lori A. Shepherd

See Also

anninfo, annObj,bandinfo, iGGV

Examples


library("iGenomicViewer")

#
# The following code will build the same object as data(annObj)
#

# writes out text files to use
writeExFiles()

# loads a band.info object
data(Band.Info)

# makes anninfo object for cancerGenes
annotation1 = makeAnnotation(file="CancerGenes.txt", file.sep="\t", label=2, chrom=3,chrom.levels=c("chr1","chr2","chr3","chr4","chr5","chr6","chr7","chr8","chr9","chr10","chr11","chr12","chr13","chr14","chr15","chr16","chr17","chr18","chr19","chr20","chr21","chr22","chrX","chrY"),band.info=band.info,  loc=NA, loc.start=4, loc.stop=5, additional=0, header=TRUE, links=6)

# makes anninfo object for DiseaseGenes
annotation2 = makeAnnotation(file="DiseaseGenes.txt", file.sep="\t", label=2, chrom=3,chrom.levels=c("chr1","chr2","chr3","chr4","chr5","chr6","chr7","chr8","chr9","chr10","chr11","chr12","chr13","chr14","chr15","chr16","chr17","chr18","chr19","chr20","chr21","chr22","chrX","chrY"),band.info=band.info, loc=NA, loc.start=4, loc.stop=5, additional=0, header=TRUE, links=7)

# makes anninfo object for DNArepairGenes
annotation3 = makeAnnotation(file="DNArepairgenes.txt", file.sep="\t", label=1, chrom=2, chrom.levels=c("chr1","chr2","chr3","chr4","chr5","chr6","chr7","chr8","chr9","chr10","chr11","chr12","chr13","chr14","chr15","chr16","chr17","chr18","chr19","chr20","chr21","chr22","chrX","chrY"), band.info=band.info, loc=NA, loc.start=3, loc.stop=4, additional=0, header=TRUE, links=5)

# take individual anninfo objects and create a master annotation object 
annObj = annotationObj(annotation1, obj.name="CancerGenes")
annObj = annotationObj(annotation2, annotationObj=annObj, obj.name="DiseaseGenes")
annObj = annotationObj(annotation3, annotationObj=annObj, obj.name="DNArepairGenes")



[Package iGenomicViewer version 2.4.6 Index]