mappingObj {iGenomicViewer}R Documentation

Creates Mapping Object

Description

This function creates a mapping object

Usage

mappingObj(file,
          spot.ID,
          chrom,
          chrom.levels,
          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,
          band.info = NA,
          returnVl = TRUE,
          saveFile = FALSE,
          saveName="MapObj.RData",
          ...)

mappingObjMarray(obj,
                 spot.ID=NA,
                 chrom,
                 locBy,
                 base.chrm=NA,
                 reg.exp=NA,           
                 loc=NA,
                 loc.start=NA,
                 loc.stop=NA,
                 additional=NA,
                 names.additional=NA,
                 links=NA,
                 names.links=NA,
                 images=NA,
                 names.images=NA,
                 band.info = NA,
                 returnVl = TRUE,
                 saveFile = FALSE,
                 saveName="MapObj.RData")
 
mappingObjADF(adf,
              spot.ID=NA,
              chrom,
              locBy,
              base.chrm=NA,
              reg.exp=NA,           
              loc=NA,
              loc.start=NA,
              loc.stop=NA,
              additional=NA,
              names.additional=NA,
              links=NA,
              names.links=NA,
              images=NA,
              names.images=NA,
              band.info = NA,
              returnVl = TRUE,
              saveFile = FALSE,
              saveName="MapObj.RData")


mappingObjDF(df,
             spot.ID=NA,
             chrom,
             locBy,
             base.chrm=NA,
             reg.exp=NA,           
             loc=NA,
             loc.start=NA,
             loc.stop=NA,
             additional=NA,
             names.additional=NA,
             links=NA,
             names.links=NA,
             images=NA,
             names.images=NA,
             band.info = NA,
             returnVl = TRUE,
             saveFile = FALSE,
             saveName="MapObj.RData")



Arguments

file path name of file
obj object of the class marrayInfo, marrayRaw or marrayNorm
adf annotated data frame object
df data frame object
spot.ID column in file or object that represents spot.IDs i.e. clone, BAC
chrom column in file or object that represents the chromosome location
chrom.levels vector indicating how the chrom column is represented. i.e chr1, chrom1, 1, etc.
base.chrm vector of characters to be replaced in chromosome to achieve numeric vector
reg.exp logical indication if base.chrm entry is exact match or should be used in perl regular expression mapping
loc column in file or object representing genomic location. See details for more information
loc.start column in file or object representing starting genomic location. See details for more information
loc.stop column in file or object representing ending genomic location. See details for more information
locBy either within or across to represent if the genomic locations are within, with respect to, chromosome or across the entire genomic.
file.sep seperation character for file
additional indication of additional columns in file or object that should be included in mapping object
names.additional optional header names for additional columns to be included
links indication of columns in file or object that represent hyperlinks, character or numeric, or a data.frame, with rows equal to the number of rows of the file, of hyperlinks that must be in the same order as they appear in the file
names.links optional header names for links
images indication of columns in file or object 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
band.info a band.info object. see makeBandInfo
returnVl logical indicating if object created should be returned
saveFile logical indicating if object created should be saved to a file
saveName if saveVl, path name of file
... additional arguments to the read.table function for reading the file

Details

The mapping 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 mapping 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 be displayed using the images argument.

Value

an object of the class mapobj which contains mapping and band information

Author(s)

Lori A. Shepherd

See Also

mapobj, mapping.info, bandinfo, iGGV

Examples


#
# The following code will build the same object as data(mapping.info)
#

library("iGenomicViewer")

# writes out text files to use
writeExFiles()

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

# make mapping information object
mapping.info = mappingObj(file="HB19Kv2.HG18.txt", spot.ID="Clone", chrom="Chromosome",  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"),loc.start="start", loc.stop="Stop", file.sep="\t", additional=c("Mapped.by", "Flag"), band.info=band.info, header=TRUE, returnVl=TRUE, links=10, names.links="UCSC")


[Package iGenomicViewer version 2.4.6 Index]