Search
Question: Subsetting samples and columns of a MethyLumiSet subsets QC probes
1
gravatar for alan.ocallaghan
12 months ago by
alan.ocallaghan10 wrote:

Loading 450k methylation data as follows: methyset <- methylumIDAT(barcodes=barcodes, parallel=TRUE, idatPath="./data/IDATS")

Then the following code will error (subscript out of bounds): methyset[1:1000, 1:2]

This is because there are only 850 QC probes, which should not be subset with the indices used on the main dataset.

The code responsible is below: https://github.com/Bioconductor-mirror/methylumi/blob/master/R/MethyLumiSet-class.R#L454

ADD COMMENTlink modified 12 months ago by Sean Davis21k • written 12 months ago by alan.ocallaghan10
0
gravatar for Sean Davis
12 months ago by
Sean Davis21k
United States
Sean Davis21k wrote:

Thanks for the report. This should be fixed in 2.24.1 (release) and 2.25.1 (devel) versions.

ADD COMMENTlink written 12 months ago by Sean Davis21k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 361 users visited in the last hour