search

rezakj / iCellR

Single (i) Cell R package (iCellR) is an interactive R package to work with high-throughput single cell sequencing technologies (i.e scRNA-seq, scVDJ-seq, scATAC-seq, CITE-Seq and Spatial Transcriptomics (ST)).
120 stars 19 forks source link

VDJ data loading #11

Closed jsmoon4 closed 4 years ago

jsmoon4 commented 4 years ago

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 4 years ago

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 4 years ago

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

rezakj commented 4 years ago

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".