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bmansfeld / QTLseqr

QTLseqr is an R package for QTL mapping using NGS Bulk Segregant Analysis
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Unknown or uninitialised column: 'CHROM' #7

Closed biopig closed 6 years ago

biopig commented 6 years ago

when i'm useing the qtlseqr, and i have a promble, i can find the mathod my file is 'zhang'

CHROM   POS REF ALT H.AD    H.DP    H.GQ    H.PL    L.AD    L.DP    L.GQ    L.PL
Chr1    1984    T   C   19,0    19  57  0,57,956    10,3    13  87  87,0,420
Chr1    1994    C   T   19,1    20  34  0,34,532    10,4    14  61  61,0,297
Chr1    1995    G   A   21,0    21  63  0,63,1046   11,3    14  84  84,0,436
Chr1    2025    G   A   20,7    27  99  128,0,515   17,4    21  75  75,0,515
Chr1    2031    C   T   31,0    31  93  0,93,1355   19,5    24  76  76,0,667
Chr1    16386   C   A   3,2 5   75  75,0,140    6,0 6   18  0,18,250
Chr1    16402   TA  T   5,0 5   15  0,15,185    3,2 5   49  49,0,106
Chr1    16417   G   C   5,2 7   69  69,0,187    7,0 7   21  0,21,277
Chr1    17148   T   A   16,6    22  68  68,0,526    18,0    18  60  0,60,663
high<-"H"
low<-"L"
df<-importFromGATK(file="zhang",highBulk=high,lowBulk=low,chromList="Chr1")
Parsed with column specification:
cols(
  CHROM = col_integer(),
  POS = col_integer(),
  REF = col_character(),
  ALT = col_character(),
  H.AD = col_character(),
  H.DP = col_integer(),
  H.GQ = col_integer(),
  H.PL = col_character(),
  L.AD = col_character(),
  L.DP = col_integer(),
  L.GQ = col_integer(),
  L.PL = col_character()
)
Removing the following chromosomes: 
Warning messages:
1: Unknown or uninitialised column: 'CHROM'. 
2: Unknown or uninitialised column: 'CHROM'. 
3: Unknown or uninitialised column: 'CHROM'. 
4: Length of logical index must be 1 or 99, not 0 
5: Unknown or uninitialised column: 'CHROM'. 
6: Unknown or uninitialised column: 'CHROM'.
biopig commented 6 years ago

@bmansfeld

bmansfeld commented 6 years ago

Hi, For some reason the readr::read_tsv function is interpreting you CHROM column as an integer: See:

Parsed with column specification:
cols(
  CHROM = col_integer(),

It is hard for me to understand why without your full data file. If you would like, and feel comfortable sending me the actual file you can: mansfeld (at) msu.edu Ben

biopig commented 6 years ago

what is you email

biopig commented 6 years ago

@bmansfeld i have send my file to you email

bmansfeld commented 6 years ago

Hi, I did not receive the file. Perhaps it was too large to send. I recommend uploading it to a Dropbox or drive and sharing a link we me. Thanks

bmansfeld commented 6 years ago

Hello, Thanks for sending your file. I have figured out the problem. Since your bulks were named "H" and "L" and there is a column renaming step in the import function, the H in CHROM was being renamed to HIGH. I have fixed this in the current v 0.6.5. Thanks for helping me find this bug. Ben