From 560ef0af863a721583b156fe5dd5006aa7638dbc Mon Sep 17 00:00:00 2001
From: Alex Sickler <sicklera@chop.edu>
Date: Thu, 2 Feb 2023 10:04:44 -0500
Subject: [PATCH] :fire: remove calls to deprecated functions

---
 .../02-calculate-methly-quantiles.R                    | 10 +++++-----
 .../05-create-methyl-summary-table.R                   |  8 ++++----
 2 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/analyses/methylation-summary/02-calculate-methly-quantiles.R b/analyses/methylation-summary/02-calculate-methly-quantiles.R
index 83933322a3..b1916add2c 100755
--- a/analyses/methylation-summary/02-calculate-methly-quantiles.R
+++ b/analyses/methylation-summary/02-calculate-methly-quantiles.R
@@ -62,7 +62,7 @@ histologies <- data.table::fread(histologies, sep = "\t",
 
 # Get methyl values and only keep samples in independent sample list
 methyl_matrix_df <- readr::read_rds(methyl_matrix) %>%
-  dplyr::select(tidyselect::any_of(c("Probe_ID", independent_samples)))
+  dplyr::select(c("Probe_ID", independent_samples))
 
 # Calculating probe-level methyl values quantiles for all pre-processed samples
 message("===============================================================")
@@ -83,8 +83,8 @@ for (dataset in unique(histologies$cohort)) {
       dplyr::pull(Kids_First_Biospecimen_ID) 
     quantiles <- methyl_matrix_df %>% 
       tibble::column_to_rownames(var = "Probe_ID") %>% 
-      dplyr::select(any_of(sample_ids)) %>% 
-      dplyr::filter(if_any(everything(), ~ !is.na(.))) %>% 
+      dplyr::select(sample_ids) %>%
+      na.omit() %>%
       apply(1, quantile, na.rm = TRUE) %>% t() %>% 
       tibble::as_tibble(rownames = "Probe_ID")
     if (methyl_values == "beta"){  
@@ -111,13 +111,13 @@ if (methyl_values == "beta"){
   methyl_quantiles %>% data.table::setDT() %>%
   data.table::fwrite(file.path(results_dir, 
                                "methyl-probe-beta-quantiles.tsv.gz"), 
-                     sep="\t", compress = "auto")
+                     sep="\t")
 } else {
   message("Writing probe-level methyl values quantiles to methyl-probe-m-quantiles.tsv file...\n")
   methyl_quantiles %>% data.table::setDT() %>%
     data.table::fwrite(file.path(results_dir, 
                                  "methyl-probe-m-quantiles.tsv.gz"), 
-                       sep="\t", compress = "auto")  
+                       sep="\t")
 }
 
 message("Analysis Done..\n")
diff --git a/analyses/methylation-summary/05-create-methyl-summary-table.R b/analyses/methylation-summary/05-create-methyl-summary-table.R
index 2add128564..232bd6fddd 100755
--- a/analyses/methylation-summary/05-create-methyl-summary-table.R
+++ b/analyses/methylation-summary/05-create-methyl-summary-table.R
@@ -152,7 +152,7 @@ if (exp_values == "gene") {
     methy_summary_table %>% data.table::setDT() %>%
       data.table::fwrite(file.path(results_dir,
                                    "gene-methyl-beta-values-summary.tsv.gz"), 
-                         sep="\t", compress = "auto")
+                         sep="\t")
   } else {
     methy_summary_table <-  methy_summary_table %>% 
       dplyr::select(Gene_symbol, targetFromSourceId, Dataset, Disease,
@@ -163,7 +163,7 @@ if (exp_values == "gene") {
     methy_summary_table %>% data.table::setDT() %>%
       data.table::fwrite(file.path(results_dir,
                                    "gene-methyl-m-values-summary.tsv.gz"), 
-                         sep="\t", compress = "auto")
+                         sep="\t")
   }
 } else {
   if (methyl_values == "beta") {
@@ -177,7 +177,7 @@ if (exp_values == "gene") {
     methy_summary_table %>% data.table::setDT() %>%
       data.table::fwrite(file.path(results_dir,
                                    "isoform-methyl-beta-values-summary.tsv.gz"), 
-                         sep="\t", compress = "auto")
+                         sep="\t")
   } else {
     methy_summary_table <-  methy_summary_table %>% 
       dplyr::select(Gene_symbol, targetFromSourceId, transcript_id, Dataset,
@@ -189,7 +189,7 @@ if (exp_values == "gene") {
     methy_summary_table %>% data.table::setDT() %>%
       data.table::fwrite(file.path(results_dir,
                                    "isoform-methyl-m-values-summary.tsv.gz"), 
-                         sep="\t", compress = "auto")
+                         sep="\t")
   }
 } 
 message("Analysis Done..\n")
\ No newline at end of file