Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

invalid class “ScoreMatrix” object #191

Open
LiyanJi-code opened this issue Jun 9, 2020 · 1 comment
Open

invalid class “ScoreMatrix” object #191

LiyanJi-code opened this issue Jun 9, 2020 · 1 comment

Comments

@LiyanJi-code
Copy link

## When I run the code as below, I got an error. Could you help me deal with the bugs? Thanks a lot.
data(cage)
data(promoters)
scores1=ScoreMatrix(target=cage,windows=promoters,strand.aware=TRUE,
weight.col="tpm")

library(GenomicRanges)
covs = coverage(cage)
scores2 = ScoreMatrix(target=covs,windows=promoters,strand.aware=TRUE)
scores2

bam.file = system.file('unitTests/test.bam', package='genomation')
windows = GRanges(rep(c(1,2),each=2), IRanges(rep(c(1,2), times=2), width=5))
scores3 = ScoreMatrix(target=bam.file,windows=windows, type='bam')
scores3

Error in validObject(.Object) :
invalid class “ScoreMatrix” object: superclass "vector_OR_Vector" not defined in the environment of the object's class

sessionInfo()
R version 3.6.0 (2019-04-26)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS release 6.9 (Final)

@katwre
Copy link
Contributor

katwre commented Jun 9, 2020

Hi @Julian-jly ,

what version of genomation are you using? I just quickly checked your code, and for me, it works just fine. Do you use S4Vectors package version >= 0.17.25 ?

Kasia

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

2 participants