search for: bamfile

...ad the code from a file, using source(). Then I execute it fine. Then I remove the function object, I load the package, and execute the same code from the package - and I get an error. Please help! Mick > library(Rsamtools) > source("viRome/R/read.bam.R") > read.bam function(bamfile=NULL, chr=NULL, start=1, end=1e07, what=c("qname", "flag", "rname", "strand", "pos", "qwidth", "mapq", "cigar", "mrnm", "mpos", "isize", "seq"), tag=c("NM&quo...

Hello, Can anyone please suggest any packages in R that can be used to overlay gene expression data on SNP (affymetrix) copy number ? Thanks, Ekta Senior Research Associate Bioinformatics Department Jubilant Biosys Pvt Ltd, #96, Industrial Suburb, 2nd Stage Yeshwantpur, Bangalore 560 022 Ph No : +91-80-66628346 The information contained in this electronic message and in any attachments to this

...cular view? net work? and what format your data are? for example, in ggbio, it depends on what data you are using, you can arrange your data into GRanges manually or just provide data that rtracklayer supported like bed, then just use autoplot, it accepts different objects, like GRanges, IRanges, bamfiles or character... allow some transformation like coverage. For files like bed, it automatically use bar to represent your data and use score as y(you can specify other y). Function tracks() allow you to bind or overlay any graphics produced by ggbio or ggplot2, so you could work from data.frame too,...