Question: question about DiffBind
1
gravatar for mikysyc2016
16 months ago by
mikysyc201660
mikysyc201660 wrote:

Hi all,

I get the error from R, when I try to use DiffBind. Do not understand what is this?

tamoxifen <- dba(sampleSheet="tamoxifen.csv", dir(path = system.file("extra", package="DiffBind")))

Error in dba(sampleSheet = "tamoxifen.csv", dir(path = system.file("extra",  : 
  DBA object is a character string; perhaps meant to be argument 'sampleSheet'?

Thanks!

chip-seq R • 694 views
ADD COMMENTlink modified 16 months ago by zx87548.2k • written 16 months ago by mikysyc201660
2
gravatar for Federico Giorgi
16 months ago by
Columbia University
Federico Giorgi500 wrote:

Hi there,

I believe you are using a not up-to-date example. In DiffBind 2.4.0+ you achieve what you want to do (i.e. loading the example sample sheet) like this:

library(DiffBind)
setwd(system.file("extra", package="DiffBind"))
tamoxifen <- dba(sampleSheet="tamoxifen.csv")

Check ?dba for all details

ADD COMMENTlink modified 16 months ago • written 16 months ago by Federico Giorgi500

Hi, I use your suggestion, it works for tamoxifen samples ( which is an example of DiffBind). When i do my data analysis, i met another problem. Do you know how to deal with it?

setwd(system.file("extra_1", package="DiffBind")) ppara <- dba(sampleSheet="ppara.csv") 1 FAT ppara wt 1 bed Error in if file.info(peaks)$size > 0) { : missing value where TRUE/FALSE needed

Thanks!

ADD REPLYlink modified 16 months ago • written 16 months ago by mikysyc201660

This is telling DiffBind to look in a specific directory within the package installation for the samplesheet file. This is very non-standard -- it only looks there for the example samplesheet as this is part of the installation itself. The specific error is that the first peak file doe not exist where you are specifying it. If you are specifying the peak files in a relative location, they may not be found as you have changed the working directory to the installed library.

ADD REPLYlink modified 15 months ago • written 15 months ago by Rory Stark550
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