search

raerose01 / deconstructSigs

deconstructSigs
138 stars 47 forks source link

subscript out of bounds #33

Closed ZackDC closed 6 years ago

ZackDC commented 6 years ago

Hi, I want to use deconstructSigs to analyze the mutation signature of lung cancer patients with their whole exome sequencing data. I run the command following the instruction in the page "https://github.com/raerose01/deconstructSigs".

After I loaded the data, (str(dat4) 'data.frame': 9623 obs. of 5 variables: $ X : int 13 13 13 13 13 13 13 13 13 13 ... $ Chr: chr "chr1" "chr1" "chr1" "chr1" ... $ End: int 2461397 2461418 2461421 3328849 3328852 3328858 3328861 3328873 3328876 3328889 ... $ Ref: chr "G" "G" "G" "C" ... $ Alt: chr "A" "C" "A" "T" ...)

I run

sigs.input <- mut.to.sigs.input(mut.ref = dat4,

  • sample.id = "X",
  • chr = "Chr",
  • pos = "End",
  • ref = "Ref",
  • alt = "Alt") I got this: Error in [<-(*tmp*, i, trimer, value = 21L) : subscript out of bounds What is the mean of "subscript out of bounds"? Can you tell me what is wrong with it? Thank you! Zack
raerose01 commented 6 years ago

Hi Zack, It's hard to guess without being able to re-create the error. It sounds like one of your ref or alt sequences may not be correct. Alternatively, could you try making your sampleID column a string rather than int? If that doesn't work, can you send me a sample file that generates the error and I'll have a look. Thanks, Rachel

ZackDC commented 6 years ago

Hi Rachel,

Thank you very much for the reply!

I still can not find what is wrong with the ref or alt sequences.

The attachment is my data.

Thank you!

Warm wishes!

Zack

发件人: raerose01 notifications@github.com 发送时间: 2018年6月5日 4:28:50 收件人: raerose01/deconstructSigs 抄送: Wei Yin; Author 主题: Re: [raerose01/deconstructSigs] subscript out of bounds (#33)

Hi Zack, It's hard to guess without being able to re-create the error. It sounds like one of your ref or alt sequences may not be correct. Alternatively, could you try making your sampleID column a string rather than int? If that doesn't work, can you send me a sample file that generates the error and I'll have a look. Thanks, Rachel

― You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fraerose01%2FdeconstructSigs%2Fissues%2F33%23issuecomment-394644151&data=02%7C01%7CWei.Yin%40dartmouth.edu%7C583d4e41fb0f4afcb90f08d5cac6bff4%7C995b093648d640e5a31ebf689ec9446f%7C0%7C0%7C636637877351391102&sdata=ksbhpf8Tg8prWk4tfV0hYQOrrZgu6Ce7z2Lkuhppai4%3D&reserved=0, or mute the threadhttps://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FAmE5tcpq9JD8yU2u41_8GJEIUFFLrm_Gks5t5k9SgaJpZM4UZseP&data=02%7C01%7CWei.Yin%40dartmouth.edu%7C583d4e41fb0f4afcb90f08d5cac6bff4%7C995b093648d640e5a31ebf689ec9446f%7C0%7C0%7C636637877351391102&sdata=cqDjctn9Xn0g%2F%2BGSMPvOci4Kj5mesfzRLjC6vj5lQCQ%3D&reserved=0.

raerose01 commented 6 years ago

Hi Zack,

The following code works for me. You have to make the sampleID column something other than an int.

test <- read.csv(yourFile)
test$X <- as.character(test$X)
input <- mut.to.sigs.input(test, sample.id = 'X', chr = 'Chr', pos = 'End', ref = 'Ref', alt = 'Alt')

Best,

Rachel

ZackDC commented 6 years ago

Hi Rachel,

Thank you very much for the great help!

Warm wishes!

Zack

发件人: raerose01 notifications@github.com 发送时间: 2018年6月5日 9:29:19 收件人: raerose01/deconstructSigs 抄送: Wei Yin; Author 主题: Re: [raerose01/deconstructSigs] subscript out of bounds (#33)

Hi Zack,

The following code works for me. You have to make the sampleID column something other than an int.

test <- read.csv(yourFile) test$X <- as.character(test$X) input <- mut.to.sigs.input(test, sample.id = 'X', chr = 'Chr', pos = 'End', ref = 'Ref', alt = 'Alt')

Best,

Rachel

― You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fraerose01%2FdeconstructSigs%2Fissues%2F33%23issuecomment-394730939&data=02%7C01%7Cwei.yin%40dartmouth.edu%7C75bd0cc0bfdf427c73f108d5caf0c27a%7C995b093648d640e5a31ebf689ec9446f%7C0%7C0%7C636638057781143143&sdata=egmCkNbvd%2FkKwmi6cjjniI6OQgNtD6ttquqBzmTt%2B5M%3D&reserved=0, or mute the threadhttps://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FAmE5tdmzGRXgyNJR1Q4KYmdPSXdEDtMOks5t5pW-gaJpZM4UZseP&data=02%7C01%7Cwei.yin%40dartmouth.edu%7C75bd0cc0bfdf427c73f108d5caf0c27a%7C995b093648d640e5a31ebf689ec9446f%7C0%7C0%7C636638057781143143&sdata=hjeyjFRUXqgFWamqb2H3WB%2F%2Bs6eww7EuZ8JoXlAAgi0%3D&reserved=0.