Best way to subset CellTag object

[elisafazz]

Hello,

I would like to subset my CellTag object to contain only cells that pass certain RNA QC thresholds. When I try to subset the CellTag object to contain only a list of cells, I repeatedly receive the error object of type 'S4' is not subsettable.

I would like to subset using the whitelisted.data slot. If it is not possible to subset the entire CellTag object, do you recommend a way to subset the whitelisted.data matrix, which would then be compatible with downstream clonecalling analyses?

Thank you!

[jindalk]

Hi, we do not have builtin functionality for subsetting objects. However, you can subset the bam.parse.rslt table to your desired cell barcodes and re-run processing steps starting from Section 4: Quantify the CellTag UMI Counts and Generate UMI Count Matrices.

Please do not forget to reset existing CellTag matrices to NULL before re-running processing steps:
celltag.obj@metric.filtered.count <- as(matrix(NA, 0, 0), "dgCMatrix")

[elisafazz]

Thank you, your solution worked nicely!