mappingObj {iGenomicViewer} | R Documentation |
This function creates a mapping object
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")
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 |
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.
an object of the class mapobj which contains mapping and band information
Lori A. Shepherd
mapobj
, mapping.info
, bandinfo
, iGGV
# # 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")