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non-unique values when setting 'row.names': ‘Ighv1-13’, ‘Ighv5-8’ #14

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Anna-xu408 opened this issue Dec 10, 2022 · 0 comments

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@Anna-xu408
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Hi,
when i use RCAS to process multi-samples :

WT_rep1_path <-"D:/WT_rep1.bed"
WT_rep2_path <-"D:/WT_rep2.bed"
WT_rep3_path <-"D:/WT_rep3.bed"
KO_rep1_path <-"D:/KO_rep1.bed"
KO_rep2_path <-"D:/KO_rep2.bed"
KO_rep3_path <-"D:/KO_rep3.bed"
projData <- data.frame('sampleName' = c('WT_1', 'WT_2','WT_3' 'KO_1', 'KO_2','KO_3'),
'bedFilePath' = c(WT_rep1_path, WT_rep2_path, WT_rep3_path
KO_rep1_path,
KO_rep2_path,KO_rep3_path),
stringsAsFactors = FALSE)
projDataFile <- "D:/myProjDataFile.tsv"
write.table(projData, projDataFile, sep = '\t', quote =FALSE, row.names = FALSE)
gtfFilePath <- "D:/Mus_musculus.GRCm38.102.gtf"
databasePath <-"D:/myProject.sqlite"
createDB(dbPath = databasePath, projDataFile = projDataFile, gtfFilePath = gtfFilePath, genomeVersion = 'mm10',update = TRUE,motifAnalysis = FALSE)

it show error:
Importing GTF annotations
importing gtf file from D:/Mus_musculus.GRCm38.102.gtf
Keeping standard chromosomes only
File D:/Mus_musculus.GRCm38.102.gtf.granges.rds already exists.
Use overwriteObjectAsRds = TRUE to overwrite the file
Parsing transcript features
|++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=02m 50s
Saving interval datasets in 'bedData' table
Calculating annotation summaries
|++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=02m 28s
Saving annotation summaries in 'annotationSummaries' table
Running function: getIntervalOverlapMatrix for tablegeneOverlaps
|++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=14s
Error in .rowNamesDF<-(x, value = value) :
duplicate 'row.names' are not allowed
In addition: Warning message:
non-unique values when setting 'row.names': ‘Ighv1-13’, ‘Ighv5-8’

i think my row.name is unique? so it is why?

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