Error when run DoAbsolute in allelic mode using example data.

[lincj1994]

Hi. I've run DoAbsolute utilizing the example data. Here present the code.

example_path = system.file("extdata", package = "DoAbsolute", mustWork = T)
# segmentation file
seg_normal =  file.path(example_path, "SNP6_blood_normal.seg.txt")
seg_solid  =  file.path(example_path, "SNP6_solid_tumor.seg.txt")
seg_metastatic  = file.path(example_path, "SNP6_metastatic_tumor.seg.txt")
# MAF file
maf_solid  = file.path(example_path, "solid_tumor.maf.txt")
maf_metastatic  = file.path(example_path, "metastatic_tumor.maf.txt")

# read data
seg_normal = fread(seg_normal)
seg_solid = fread(seg_solid)
seg_metastatic = fread(seg_metastatic)
maf_solid = fread(maf_solid)
maf_metastatic = fread(maf_metastatic)

# merge data
Seg = Reduce(rbind, list(seg_normal, seg_solid, seg_metastatic))
Maf = Reduce(rbind, list(maf_solid, maf_metastatic))

Seg$Sample = substr(Seg$Sample, 1, 15)
Maf$Tumor_Sample_Barcode = substr(Maf$Tumor_Sample_Barcode, 1, 15)

# test function
DoAbsolute(Seg = Seg, Maf = Maf, platform = "SNP_6.0", copy.num.type = "allelic",
           results.dir = "test", keepAllResult = TRUE, verbose = TRUE)

Here is the Warning message

-> Setting results directory as test 
-> Loading segmentation data...
-> Loading Maf data...
-> Checking data format of segmentation file...
-> Keeping only chr 1-23 for CNV data...
-> Keeping only chr 1-23 for Maf data...
-> Creating temp directory ...
-> Setting temp directory as C:\Users\ADMINI~1\AppData\Local\Temp\RtmpSMtjMh/Absolute 
-> Spliting seg data of samples to different files...
--> Processing sample  TCGA-DK-A1A6-10 ...
---> This sample has not Maf data, skipping...
--> Processing sample  TCGA-DK-A1A6-01 ...
---> Filtering mutations which vaf< 0.1 ...
---> Filtering Maf which count< 5 ...
---> Outputing corresponding Maf file...
--> Processing sample  TCGA-DK-A1A6-06 ...
---> Filtering mutations which vaf< 0.1 ...
---> Filtering Maf which count< 5 ...
---> Outputing corresponding Maf file...
-> Spliting seg data of samples done.
-> Running RunAbsolute...(be patient)
--> Processing sample  TCGA-DK-A1A6-10 ...
----> Error detected, see log for more details.
--> Processing sample  TCGA-DK-A1A6-01 ...
----> Error detected, see log for more details.
--> Processing sample  TCGA-DK-A1A6-06 ...
----> Error detected, see log for more details.
-> RunAbsolute done. Retrieving results...
--> Files in cache directory:
[1] "tmp"
-> Checking result files...
Warning in DoAbsolute(Seg = Seg, Maf = Maf, platform = "SNP_6.0", copy.num.type = "allelic",  :
  --> Result file C:\Users\ADMINI~1\AppData\Local\Temp\RtmpSMtjMh/Absolute/cache/TCGA-DK-A1A6-10.ABSOLUTE.RData does not exist, drop it.
Warning in DoAbsolute(Seg = Seg, Maf = Maf, platform = "SNP_6.0", copy.num.type = "allelic",  :
  --> Result file C:\Users\ADMINI~1\AppData\Local\Temp\RtmpSMtjMh/Absolute/cache/TCGA-DK-A1A6-01.ABSOLUTE.RData does not exist, drop it.
Warning in DoAbsolute(Seg = Seg, Maf = Maf, platform = "SNP_6.0", copy.num.type = "allelic",  :
  --> Result file C:\Users\ADMINI~1\AppData\Local\Temp\RtmpSMtjMh/Absolute/cache/TCGA-DK-A1A6-06.ABSOLUTE.RData does not exist, drop it.
Error in DoAbsolute(Seg = Seg, Maf = Maf, platform = "SNP_6.0", copy.num.type = "allelic",  : 
  No result file to proceed.

And the error log:

Detected error in sample TCGA-DK-A1A6-10 
Error message: bad restore file magic number (file may be corrupted) -- no data loaded 
Where:
load seg.dat.fn 
Skipping this sample.
========
Detected error in sample TCGA-DK-A1A6-01 
Error message: bad restore file magic number (file may be corrupted) -- no data loaded 
Where:
load seg.dat.fn 
Skipping this sample.
========
Detected error in sample TCGA-DK-A1A6-06 
Error message: bad restore file magic number (file may be corrupted) -- no data loaded 
Where:
load seg.dat.fn 
Skipping this sample.
========

Same error when run DoAbsolute on my own data.

[ShixiangWang]

The allelic mode requires allele-specific segmentation processing before using ABSOLUTE.

[lincj1994]

Do you refer to something like the ASCAT output? I'm curious if you could provide examples of allelic-specific data. Are there specific specifications for the column names?

[ShixiangWang]

Yes.

No, I haven't the example data for allele-specific analysis. The official website of ABSOLUTE should be located at https://software.broadinstitute.org/cancer/cga/, I don't know why I cannot access it.