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ShixiangWang / DoAbsolute

:package: Automate Absolute Copy Number Calling using 'ABSOLUTE' package
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Error in DoAbsolute(Seg = Seg, Maf = Maf, platform = "Illumina_WES", copy.num.type = "total", : #11

Closed JianGuoZhou3 closed 4 years ago

JianGuoZhou3 commented 4 years ago

Hi Shixiang, I used your package for glioma_msk_2018.tar.gz. However, there are errors.

setwd("/home/xjqqqrza/jianguozhou/maftool.cao/glioma_msk_2018")
 seg =  file.path(getwd(), "data_clinical_sample1.txt") # SAMPLE_ID 改为Sample
# read data
 Seg = fread(seg)
 maf = file.path(getwd(), "data_mutations_mskcc.txt") 
 Maf = fread(maf)
 # test function
DoAbsolute(Seg = Seg, Maf = Maf, platform = "Illumina_WES", copy.num.type = "total", results.dir = getwd(), nThread = 2, keepAllResult = TRUE, verbose = TRUE)

-> Loading segmentation data...
-> Loading Maf data...
-> Checking data format of segmentation file...
Error in DoAbsolute(Seg = Seg, Maf = Maf, platform = "Illumina_WES", copy.num.type = "total",  : 
  Columns Sample Chromosome Start End Num_Probes Segment_Mean are should in file.
ShixiangWang commented 4 years ago

See the correct format:

> head(Seg)
            Sample Chromosome     Start       End Num_Probes Segment_Mean
1: TCGA-DK-A1A6-10          1   3218610 247813706     128988      -0.0029
2: TCGA-DK-A1A6-10          2    484222 242476062     131151      -0.0003
3: TCGA-DK-A1A6-10          3   2212571 197538677     106255       0.0008
4: TCGA-DK-A1A6-10          4   1053934 188763651     102639      -0.0004
5: TCGA-DK-A1A6-10          5    914233 106361340      55493       0.0000
6: TCGA-DK-A1A6-10          5 106363192 106370006          5      -1.0146

Your Seg is invalid.

JianGuoZhou3 commented 4 years ago

Thanks a lot. Best,

在 2020年7月7日，12:45，Shixiang Wang notifications@github.com 写道：

See the correct format:

head(Seg) Sample Chromosome Start End Num_Probes Segment_Mean 1: TCGA-DK-A1A6-10 1 3218610 247813706 128988 -0.0029 2: TCGA-DK-A1A6-10 2 484222 242476062 131151 -0.0003 3: TCGA-DK-A1A6-10 3 2212571 197538677 106255 0.0008 4: TCGA-DK-A1A6-10 4 1053934 188763651 102639 -0.0004 5: TCGA-DK-A1A6-10 5 914233 106361340 55493 0.0000 6: TCGA-DK-A1A6-10 5 106363192 106370006 5 -1.0146 Your Seg is invalid.

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