Starcode issue with CellTag object of 12 samples and binarization error

[FengHuu]

I have 12 different samples generated from the same starting pool of cells (same CellTag V1 labeling). I created the CellTag object by reading the 12 bam files in the correct order and proceeded to the starcode step.

Issue 1:
12 collapsing files with suffix Sample-1, Sample-2, ...., Sample-12 were generated and I starcoded them one-by-one and put the resulting files in one folder:
collapsing_result_Sample-1.txt
collapsing_result_Sample-2.txt
collapsing_result_Sample-3.txt
collapsing_result_Sample-4.txt
collapsing_result_Sample-5.txt
collapsing_result_Sample-6.txt
collapsing_result_Sample-7.txt
collapsing_result_Sample-8.txt
collapsing_result_Sample-9.txt
collapsing_result_Sample-10.txt
collapsing_result_Sample-11.txt
collapsing_result_Sample-12.txt

However, when doing
My.obj <- CellTagDataPostCollapsing(celltag.obj = My.obj, collapsed.rslt.file = list.files(collapsed.rslt.dir, full.names = T))
The collapsing result files were processed in the wrong order as:
collapsing_result_Sample-1.txt
collapsing_result_Sample-10.txt
collapsing_result_Sample-11.txt
collapsing_result_Sample-12.txt
collapsing_result_Sample-2.txt
collapsing_result_Sample-3.txt
collapsing_result_Sample-4.txt
collapsing_result_Sample-5.txt
collapsing_result_Sample-6.txt
collapsing_result_Sample-7.txt
collapsing_result_Sample-8.txt
collapsing_result_Sample-9.txt

which gave me different sample order in the collapsed.count matrix, following Sample-1 is Sample-10 but not Sample-2.

I tried rename the collapsing result files for the code to process from 1-10, still, however, after collapsing, the order in collasped.count matrix is still the same wrong order (as the picture shown above).

Issue 2:

I tried to skip starcode and proceeded to binarization
My.obj <- SingleCellDataBinarization(My.obj, 2)
which give me this error:

Error in if (any(i < 0L)) { : missing value where TRUE/FALSE needed
In addition: Warning message:
In int2i(as.integer(i), n) : NAs introduced by coercion to integer range

This error also showed up when I did binarization with the collapsed.count matrix though the order is wrong.

Please indicate:

1. does it matter that the collapsed.count matrix order is not strictly from 1 to 12? If it matters, how to correct this?
2. How to fix the binarization error?

Many thanks!
Feng