I've had a hard time finding it, but is there a jmosaics package that is version 1.1.0? I've been trying to find it and had old code that required it's use for chipseq.
http://www.bioconductor.org/packages//2.13/bioc/html/jmosaics.html The package binary (zip) listed here doesn't actually contain all the needed functions to run tutorial code, for example:
> bin1 <- readBins(type = c("chip","input"),
+ fileName = c(system.file(file.path("extdata","h3k27me3_chip_chr10.txt"),
Info: reading and preprocessing bin-level data...
Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, :
line 1 did not have 3 elements
Upon inspecting the package, the namespace has the following contents:
The R directory doesn't have the functions I'm looking for, as far as I can tell and I can't pull up documentation for the readBins function.
So the key question is... where is the old version (1.1.0) that actually had all the functions needed to run the tutorial code? I can't get the old versions because the bioconductor github mirror doesn't have the file any longer.