Comments (1)
Hi Ferdinando,
Thanks for reaching out. For your questions:
(1) In STAARpipeline_Null_Model.r
, the phenotype
object is an R data frame consisting of the sample id, covariates, and the tested phenotype. The rows of the data frame represent different individuals, and the columns represent different variables. An example of the phenotype
object can be found here.
(2) The sparse GRM can be calculated using standard approaches. An example pipeline for producing the sparse GRM from the gds file can be found here.
Please feel free to let me know if you have any additional questions. We are planning to include more explanations of the tutorial in the near future.
Best,
Xihao
from staarpipeline-tutorial.
Related Issues (20)
- vcf to gds HOT 7
- #SNVs per case/control? HOT 1
- fit_nullmodel Output is mostly Null and 0 HOT 16
- Fitting NULL model for binary outcomes HOT 5
- Error in Gene Centric Analysis HOT 1
- Error in results_plof_genome[, "cMAC"] : subscript out of bounds HOT 2
- Followup Question to Issue #28 HOT 2
- STAARpipeline_Gene_Centric_Noncoding HOT 2
- Dynamic Window dim(X) error HOT 3
- Can't annotate individual variant results HOT 2
- [Suggestion-Implementation] Add information to summary and annotations of results HOT 1
- Conditional analysis - Summary Gene Centric Noncoding not running to completion HOT 6
- Ukbiobank Agds files generation HOT 16
- 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
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from staarpipeline-tutorial.