'x' must be an array of at least two dimensions #7
Description
Dear author, I encountered the following error while running the command. Could you please provide me with some guidance? Thank you.
> res = do_pipeline(
+ out_path ="/data/polyApipe/LUAD",
+ counts_file_dir = "/data/polyApipe/LUAD/polyAbam_counts/",
+ batch_names =c("BT1290","BT1291"),
+ peak_info_file="polyAbam_polyA_peaks.gff",
+ organism ="human_ens100",
+ cells_to_use =cells_to_use,
+ cell_name_func=cell_name_func
+ )
-- 1/4 load --
Loading /data/polyApipe/LUAD/polyAbam_counts//BT1290.tab.gz
Loaded 139654 x 1276 matrix of counts
Loading /data/polyApipe/LUAD/polyAbam_counts//BT1291.tab.gz
Loaded 180737 x 1292 matrix of counts
-- 2/4 assign --
-- 3/4 weitrices --
422517 peaks in 2568 cells
Error in rowSums(assay(peaks_se_relevant, "counts")[, good_cells, drop = F] > :
'x' must be an array of at least two dimensions
In addition: Warning message:
In .merge_two_Seqinfo_objects(x, y) :
Each of the 2 combined objects has sequence levels not in the other:
- in 'x': chrM, GL000008.2, GL000009.2, GL000194.1, GL000195.1, GL000205.2, GL000213.1, GL000216.2, GL000218.1, GL000219.1, GL000220.1, GL000221.1, GL000224.1, GL000225.1, KI270330.1, KI270438.1, KI270442.1, KI270466.1, KI270467.1, KI270512.1, KI270706.1, KI270707.1, KI270708.1, KI270709.1, KI270711.1, KI270712.1, KI270713.1, KI270714.1, KI270717.1, KI270719.1, KI270720.1, KI270722.1, KI270725.1, KI270726.1, KI270727.1, KI270728.1, KI270729.1, KI270730.1, KI270732.1, KI270733.1, KI270734.1, KI270735.1, KI270736.1, KI270737.1, KI270742.1, KI270743.1, KI270744.1, KI270745.1, KI270746.1, KI270750.1, KI270752.1, KI270754.1, KI270755.1, KI270756.1
- in 'y': chrMT, chrCHR_HG107_PATCH, chrCHR_HG109_PATCH, chrCHR_HG126_PATCH, chrCHR_HG1277_PATCH, chrCHR_HG1298_PATCH, chrCHR_HG1309_PATCH, chrCHR_HG1311_PATCH, chrCHR_HG1320_PATCH, chrCHR_HG1342_HG2282_PATCH, chrCHR_HG1362_PATCH, chrCHR_HG1384_PATCH, chrCHR_HG1395_PATCH, chr [... truncated]