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jianhong / ChIPpeakAnno

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getAllPeakSequence() incongrous length between seq and myPeakList #2

Closed millerh1 closed 4 years ago

millerh1 commented 4 years ago

Hello -- I wanted to share a bug I found and the solution that worked for me:

> seqNow <- getAllPeakSequence(MSC_NT_FLI1, genome = Hsapiens)
Error in `[[<-`(`*tmp*`, name, value = c(MSC_NT_FLI1_1 = "GAACCCGGCAGGGGCGGGAAGACGCAGGAGTGGGGAGGCGGAACCGGGACCCCGCAGAGCCCGGGTCCCTGCGCCCCACAAGCCTTGGCTTCCCTGCTAGGGCCGGGCAAGGCCGGGTGCAGGGCGCGGCTCCAGGGAGGAAGCTCCGGGGCGAGCCCAAGACGCCTCCCGGGCGGTCGGGGCCCAGCGGCGGCGTTCGCAGTGGAGCCGGGCACCGGGCAGCGGCCGCGGAACACCAGCTTGGCGCAGGCTTCTCGGTCAGGAACGGTCCCGGGCCTCCCGCCCGCCTCCCTCCAGCCCCTCCGGGTCCCCTACTTCGCCCCGCCAGGCCCCCACGACCCTACTTCCCGCGGCCCCGGACGCCTCCTCACCTGCGAGCCGCCCTCCCGGAAGCTCCCGCCGCCGCTTCCGCTCTGCCGGAGCCGCTGGGTCCTAGCCCCGCCGCCCCCAGTCCGCCCGCGCCTCCGGGTCCTAACGCCGCCGCTCGCCCTCCACTGCGCCCTCCCCGAGCGCGGCTCCAGGACCCCGTCGACCCGGAGCGCTGTCCTGTCGGGCCGAGTCGCGGGCCTGGGCACGGAACTCACGCTCACTCCGAGCTCCCGACGTGCACACGGCTCCCATGCGTTGTCTTCCGAGCGTCAGGCCGCCCCTACCCGTGCTTTCTGCTCTGCAGACCCTCTTCCTAGACCTCCGTCCTTTGTCCCATCGCTGCCTTCCCCTCAAGCTCAGGGCCAAGCTGTCCGCCAACCTC",  : 
  19581 elements in value to replace 19719 elements
In addition: Warning message:
In .Seqinfo.mergexy(x, y) :
  Each of the 2 combined objects has sequence levels not in the other:
  - in 'x': HSCHR1_CTG1_UNLOCALIZED, HSCHR1_CTG2_UNLOCALIZED, HSCHR1_CTG3_UNLOCALIZED, HSCHR1_CTG4_UNLOCALIZED, HSCHR1_CTG5_UNLOCALIZED, HSCHR1_CTG6_UNLOCALIZED, HSCHR1_CTG7_UNLOCALIZED, HSCHR1_CTG8_UNLOCALIZED, HSCHR1_CTG9_UNLOCALIZED, HSCHR2_RANDOM_CTG1, HSCHR2_RANDOM_CTG2, HSCHR3UN_CTG2, HSCHR4_RANDOM_CTG4, HSCHR5_RANDOM_CTG1, HSCHR9_UNLOCALIZED_CTG1, HSCHR9_UNLOCALIZED_CTG2, HSCHR9_UNLOCALIZED_CTG3, HSCHR9_UNLOCALIZED_CTG4, HSCHR11_CTG1_UNLOCALIZED, HSCHR14_CTG1_UNLOCALIZED, HSCHR14_CTG2_UNLOCALIZED, HSCHR14_CTG3_UNLOCALIZED, HSCHR14_CTG4_UNLOCALIZED, HSCHR14_CTG5_UNLOCALIZED, HSCHR14_CTG6_UNLOCALIZED, HSCHR14_CTG7_UNLOCALIZED, HSCHR14_CTG8_UNLOCALIZED, HSCHR15_RANDOM_CTG1, HSCHR16_RANDOM_CTG1, HSCHR17_RANDOM_CTG3, HSCHR17_RANDOM_CTG4, HSCHR17_RANDOM_CTG5, HSCHR22_UNLOCALIZED_CTG1, HSCHR22_UNLOCALIZED_CTG2, HSCHR22_UNLOCALIZED_CTG3, HSCHR22_UNLOCALIZED_CTG4, HSCHR22_UNLOCALIZED_CTG5, HSCHR22_UNLOCALIZED_CTG6, HSCH [... truncated]

The issue is that seq from seq <- getSeq(genome, myPeakList, as.character=TRUE) may not be the same length as myPeakList. This can be fixed by adding another line: myPeakList <- myPeakList[names(myPeakList) %in% names(seq),]

Best, Henry

jianhong commented 4 years ago

Thank you.