rezakj/iCellR

VDJ data loading

jsmoon4 opened this issue · 3 comments

jsmoon4 commented

Hi, Thanks for this helpful tool.
I have a question to load VDJ data from 10X sequencing. I wanted to use prep.vdj function to load data, but the code has an error like this..
my.vdj.1 <- prep.vdj(vdj.data = "G3_all_contig_annotations.csv", cond.name = "Pre")

Error in subset.default(my.vdj, productive == "True") :
object 'productive' not found

In my data, 'productive' object exists with True and False. I don't know why this is not working.
Please let me know what is needed to be correct.
Many thanks.

rezakj commented

Would you run the example file to check. I just added an example file to the tutorial. I will soon add a full example with tutorials and more explanations. If you still get an error give me some time and I will fix it. I have been a bit busy but soon will debug more VDJ parts of the tool.

jsmoon4 commented

Sorry for late reply.
In tutorial, I just found the example file with gene expression data.
Where is VDJ data in tutorial?

rezakj commented

First update iCellR to version 1.5.8. It's not in CRAN yet so update from GitHub.

Then add your VDJ data to iCellR object
my.obj <- add.vdj(my.obj, vdj.data = my.vdj.data)

The rest is explained in detail in the updated section for plotting "How to plot clonotypes".