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Error when important data in build 36 #4

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mightyphil2000 opened this issue Jun 17, 2021 · 0 comments
Open

Error when important data in build 36 #4

mightyphil2000 opened this issue Jun 17, 2021 · 0 comments

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@mightyphil2000
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When trying to format a dataset in build 36 format I get these errors. The error seems to be a problem with liftover or with the chain file.

`

x$format_dataset()
Checking alleles are in A/C/T/G/D/I
0 variants with disallowed characters
Is this how the dataset should look?
tibble [355,736 × 8] (S3: tbl_df/tbl/data.frame)
$ chr : int [1:355736] 1 1 1 1 1 1 1 1 1 1 ...
$ pos : int [1:355736] 775852 993492 1087198 1120590 1145994 1148494 1201155 1468016 1490804 1495898 ...
$ ea : chr [1:355736] "T" "C" "T" "C" ...
$ oa : chr [1:355736] "C" "T" "G" "A" ...
$ beta: num [1:355736] -0.0202 0.1561 0.2095 -0.1335 0.0149 ...
$ se : num [1:355736] 0.129 0.105 0.188 0.161 0.136 ...
$ pval: num [1:355736] 0.875 0.138 0.265 0.407 0.911 ...
$ eaf : num [1:355736] 0.167 0.2669 0.0626 0.1023 0.1414 ...
NULL
Determining build
Only using position
# A tibble: 3 x 3
build prop_pos n_found

1 37 0.00149 530
2 38 0.00137 486
3 36 0.184 65326
Lifting build: 36 to 37
Loading chainfile
Error in h(simpleError(msg, call)) :
error in evaluating the argument 'con' in selecting a method for function 'import': invalid class “ChainFile” object: undefined class for slot "resource" ("characterORconnection")
In addition: Warning messages:
1: undefined slot classes in definition of "XRaw": elementMetadata(class "DataFrame_OR_NULL")
2: undefined slot classes in definition of "XInteger": elementMetadata(class "DataFrame_OR_NULL")
3: undefined slot classes in definition of "XDouble": elementMetadata(class "DataFrame_OR_NULL")
4: no function found corresponding to methods exports from ‘XVector’ for: ‘parallel_slot_names’
5: multiple methods tables found for ‘which’
`

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