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wevanjohnson ksmbandi aubreyodom cjlove1130 xutao-wang arun-sub anirue pyone5 mizuki0223 jessmcc22 cvn001

tbsignatureprofiler's Issues

tb-profiler collate KeyError: 'drugs'

Hi Jody,

I have been running the tb-profiler collate on all my MTBs and have not been getting any issue. But today I got this issue (refer below) that I am not sure what is the reason. I wonder if you could quickly have a look to see what is the error and how do I fix it?

Cheers,
Lex

tb-profiler error report

  • OS: linux
  • Program version: 3.0.4
  • Database version: b2af444
  • Program call:
{'prefix': '20210706', 'samples': None, 'dir': 'results', 'full': True, 'all_variants': True, 'mark_missing': False, 'reporting_af': 0.1, 'db': 'tbdb', 'external_db': None, 'func': <function main_collate at 0x7f13c45ef5e0>}

Traceback:

  File "/home/users/iidlleo/miniconda3/bin/tb-profiler", line 571, in <module>
    args.func(args)
  File "/home/users/iidlleo/miniconda3/bin/tb-profiler", line 273, in main_collate
    tbp.collate_results(args.prefix,conf,sample_file=args.samples,result_dir=args.dir,reporting_af=args.reporting_af,mark_missing=args.mark_missing)
  File "/home/users/iidlleo/miniconda3/lib/python3.8/site-packages/tbprofiler/collate.py", line 58, in collate_results
    for d in x["drugs"]:

Value:

'drugs'```

Error in mkAssay(BRCA, log = TRUE, counts_to_CPM = TRUE) : input_name must be an SE_obj assay

Hi all,

Thanks for developing such a cool package!

When I run the sample data, it worked well!
However, when I tried to use my own data, I ran into some problems. Because my metadata data and counts data are in a simple .csv format, I need to create a SummarizeExperiment () object by myself. Then I just followed this tutorial SummarizedExperiment, and did the following steps:

> coldata <- read.table("clin_metadata.csv",header = T,sep = ",", row.names=1)
> coldata[1:3,1:3]
             days_to_initial_pathologic_diagnosis last_contact_days_to death_days_to
TCGA.A8.A08L                                    0      [Not Available]            30
TCGA.UU.A93S                                    0      [Not Available]           116
TCGA.A2.A0CU                                    0      [Not Available]           158

> counts <- read.delim("counts_anno.csv", header = T, sep=",", row.names=1)
> counts[1:3,1:3]
       TCGA.A8.A08L TCGA.UU.A93S TCGA.A2.A0CU
TSPAN6         4150          351         1439
TNMD             17           36           73
DPM1           3870         1315         1683

> BRCA <- SummarizedExperiment(counts, colData = coldata)
> BRCA
class: SummarizedExperiment 
dim: 38660 55 
metadata(0):
**assays(1): ''**
rownames(38660): TSPAN6 TNMD ... HERC2P7 LINC01144
rowData names(0):
colnames(55): TCGA.A8.A08L TCGA.UU.A93S ... TCGA.B6.A0RI TCGA.B6.A0RU
colData names(6): days_to_initial_pathologic_diagnosis last_contact_days_to ...
  metastatic_tumor_indicator Treatment

**> assays(BRCA) 
List of length 1**

**> BRCA <- mkAssay(BRCA, log = TRUE, counts_to_CPM = TRUE)
Error in mkAssay(BRCA, log = TRUE, counts_to_CPM = TRUE) : 
  input_name must be an SE_obj assay**

I think I had some problems creating SummarizeExperiment(), because my assays(BRCA) only have "List of Length 1" and not "names(1): counts". But I don't know what should I do.

Any advice would be highly appreciated! Thanks!

Add example for distinctColors function

distinctColors is a function to assist users in creating color schemes for heatmaps. Currently, it lacks an example - I didn't write the function, so I'm not quite sure how it is intended to be used. It would be helpful to add an example of a coloring object being created with distinctColors, and then being used in the function call for signatureHeatmap or a similar function.

TBSignatureProfiler with microarray data?

Hi Brie,

I hop you are doing great!

A quick question: can I use TBSignatureProfiler with normalised microarray data?
Screenshot 2024-03-08 at 10 28 06

Looking forward to hearing you. Thanks.

Kind regards,
Birong

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