quantile_twas_weight.R and add functions in misc.R #258
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gaow
reviewed
Sep 26, 2024
NAMESPACE
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| @@ -15,10 +15,12 @@ export(bayes_n_rss_weights) | |||
| export(bayes_n_weights) | |||
| export(bayes_r_rss_weights) | |||
| export(bayes_r_weights) | |||
| export(calculate_qr_and_pseudo_R2) | |||
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Lets make this internal functions not to be exported.
gaow
reviewed
Sep 26, 2024
NAMESPACE
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| export(clean_context_names) | ||
| export(coloc_post_processor) | ||
| export(coloc_wrapper) | ||
| export(compute_qtl_enrichment) | ||
| export(corr_filter) |
gaow
reviewed
Sep 26, 2024
| #' @param top_percent Percentage of top SNPs to select | ||
| #' @return A list containing various results from the QR screen | ||
| #' @export | ||
| qr_screen <- function(X, Y, Z = NULL, tau.list, threshold = 0.05, method = 'qvalue', top_count = 10, top_percent = 15) { |
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let's give tau.list a default of 0.05, 0.1, etc
gaow
reviewed
Sep 26, 2024
| } | ||
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| ranks_list = lapply(tau.list, function(tau) { | ||
| suppressWarnings(rq.fit.br(zz, y, tau = tau)$dual - (1 - tau)) |
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do you know why they suppressWarning? i worry by doing so we high something funky ..
gaow
reviewed
Sep 26, 2024
R/quantile_twas_weight.R
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| } | ||
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| if (!is.null(Z)) { | ||
| xstar = lm(x ~ zz - 1)$residual |
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could you check if .lm.fit(zz,x)$residual works and give same results? This is a faster implementation than lm
gaow
reviewed
Sep 26, 2024
R/quantile_twas_weight.R
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| #' @param final_clump_r2 R-squared threshold for final LD clumping based on MAF | ||
| #' @return A list containing final SNPs and clumped SNPs | ||
| #' @export | ||
| perform_clumping_and_pruning <- function(X, qr_results, maf_list = NULL, ld_clump_r2 = 0.2, final_clump_r2 = 0.8) { |
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could you change the function name to multi_quantile_ld_clumping to better reflect what it does?
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