Comments (6)
Hi @kwdoyle,
Thank you for letting me know. Could I ask what FAVOR database files did you use to annotate your genotype data?
Best,
Xihao
from staarpipeline-tutorial.
I'm using the full database of 160 annotations hosted on Harvard Dataverse. More specifically, just the database file for chromosome 5 for now.
Interestingly enough, the Annotate.R script seems to work correctly. If I read in the saved, merged annotation file "Anno_chr5_STAARpipeline.csv" with data.table::fread, all of the data indicated in my previous post as being character-formatted are read in as numeric.
So presumably the issue occurs somewhere in the gds2agds.R script?
It also might be of interest that I chose to annotate the gds using all 160 annotations (rather, I set my 'anno_colnum' variable as c(1, 8:190). I chose the same initial annotations as the default (1 and 8) and then selected all variables from 8 to the end. I'm not sure if this is relevant, however, as the file from Annotate.R seems fine
from staarpipeline-tutorial.
Oh, while looking through the scripts, I think this part in gds2agds.R might be the problem:
FunctionalAnnotation <- read_csv(paste0(dir_anno,"chr",chr,"/",anno_file_name_1,chr,anno_file_name_2),
col_types=list(col_character(),col_double(),col_double(),col_double(),col_double(),
col_double(),col_double(),col_double(),col_double(),col_double(),
col_character(),col_character(),col_character(),col_double(),col_character(),
col_character(),col_character(),col_character(),col_character(),col_double(),
col_double(),col_character()))
The character values I'm seeing might be in the location of these hard-coded character columns..
from staarpipeline-tutorial.
Hi @kwdoyle,
Thank you so much for taking a closer look at the issue. Yes indeed, the current FAVORannotator script in the STAARpipeline-Tutorial works well for the FAVOR Essential Database hosted on Harvard Dataverse. For the full database of 160 annotations, it is recommended to adapt the col_types
in gds2agds.R to reflect the correct column type for each annotation.
Best,
Xihao
from staarpipeline-tutorial.
Yes, this was indeed the issue. If I removed the col_types specification and let read_csv auto-assign the column classes, everything seems to work fine.
from staarpipeline-tutorial.
Thank you @kwdoyle! Feel free to let me know if you have any other questions, or you may close this issue.
from staarpipeline-tutorial.
Related Issues (20)
- fit_nullmodel Output is mostly Null and 0 HOT 16
- Fitting NULL model for binary outcomes HOT 5
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- Followup Question to Issue #28 HOT 2
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- [Suggestion-Implementation] Add information to summary and annotations of results HOT 1
- Conditional analysis - Summary Gene Centric Noncoding not running to completion HOT 6
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- Plots for gene centric ncRNA regions HOT 5
- FATAL ERROR - Too many first alleles as the major allele (~21.5%). HOT 1
- warning messages in generating the annotated GDS (aGDS) file. HOT 3
- Controls / cases counts inverted when using binary model HOT 7
- kinship matrix HOT 2
- variant set in gene-centric coding/noncoding analysis HOT 2
- in the Step 2: Individual (single-variant) analysis, Error in if (chr == 1) { : argument is of length zero HOT 3
- Error : Mat::operator(): index out of bounds & Error in apply(emthr_SCANG_O, 2, max) : HOT 1
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