From 3a7ae96099b5c7b1257ed80226a9ce90915d67c5 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Fri, 3 Nov 2023 14:30:23 +0000
Subject: [PATCH 1/2] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 R/mouse_deconvolution_methods.R           | 47 ++++++++++++-----------
 tests/testthat/test_deconvolution_mouse.R |  4 +-
 2 files changed, 26 insertions(+), 25 deletions(-)

diff --git a/R/mouse_deconvolution_methods.R b/R/mouse_deconvolution_methods.R
index f735d05..4b166f0 100644
--- a/R/mouse_deconvolution_methods.R
+++ b/R/mouse_deconvolution_methods.R
@@ -260,7 +260,7 @@ deconvolute_mouse <- function(gene_expression_matrix,
 #'
 #' @export
 convert_human_mouse_genes <- function(gene_expression_matrix, mirror = "www",
-                                      other_annot = TRUE, convert_to = c('human', 'mouse')) {
+                                      other_annot = TRUE, convert_to = c("human", "mouse")) {
   gene.names <- rownames(gene_expression_matrix)
   gene_expression_matrix$gene_name <- gene.names
 
@@ -270,25 +270,25 @@ convert_human_mouse_genes <- function(gene_expression_matrix, mirror = "www",
   genes.retrieved <- NULL
   tryCatch(
     expr = {
-
-      if(convert_to == 'human'){
-        mart.use = mouse
-        mart.link = human
-        attr = 'mgi_symbol'
-        attr.link = 'hgnc_symbol'
+      if (convert_to == "human") {
+        mart.use <- mouse
+        mart.link <- human
+        attr <- "mgi_symbol"
+        attr.link <- "hgnc_symbol"
       } else {
-        mart.use = human
-        mart.link = mouse
-        attr = 'hgnc_symbol'
-        attr.link = 'mgi_symbol'
+        mart.use <- human
+        mart.link <- mouse
+        attr <- "hgnc_symbol"
+        attr.link <- "mgi_symbol"
       }
 
       genes.retrieved <<- getLDS(
         attributes = c(attr),
         filters = attr, values = gene.names,
-        mart = mart.use, attributesL = c(attr.link), martL = mart.link, uniqueRows = T)
+        mart = mart.use, attributesL = c(attr.link), martL = mart.link, uniqueRows = T
+      )
 
-      if(convert_to == 'human'){
+      if (convert_to == "human") {
         newGenes.counts <<- gene_expression_matrix %>%
           left_join(., genes.retrieved, by = c("gene_name" = "MGI.symbol")) %>%
           select(., -c("gene_name")) %>%
@@ -301,21 +301,19 @@ convert_human_mouse_genes <- function(gene_expression_matrix, mirror = "www",
       }
     },
     error = function(e) {
-
       if (other_annot) {
         print("Cannot connect to ENSEMBL. Using alternative method. This will take some time.")
         # Code adapted from: https://support.bioconductor.org/p/129636/#9144606
 
         mouse_human_genes <- read.csv("http://www.informatics.jax.org/downloads/reports/HOM_MouseHumanSequence.rpt", sep = "\t")
 
-        find_corr_gene <- function(gene, mouse_human_genes_df, convert_to = c('human', 'mouse')) {
-
-          if(convert_to == 'human'){
-            orgn.name <- 'mouse, laboratory'
-            new.orgn <- 'human'
+        find_corr_gene <- function(gene, mouse_human_genes_df, convert_to = c("human", "mouse")) {
+          if (convert_to == "human") {
+            orgn.name <- "mouse, laboratory"
+            new.orgn <- "human"
           } else {
-            orgn.name <- 'human'
-            new.orgn <- 'mouse, laboratory'
+            orgn.name <- "human"
+            new.orgn <- "mouse, laboratory"
           }
 
           class_key <- (mouse_human_genes_df %>%
@@ -330,8 +328,11 @@ convert_human_mouse_genes <- function(gene_expression_matrix, mirror = "www",
             }
 
             if (!is.null(output)) {
-              return(data.frame("new_gene" = output,
-                                "old_gene" = gene))}
+              return(data.frame(
+                "new_gene" = output,
+                "old_gene" = gene
+              ))
+            }
           }
         }
 
diff --git a/tests/testthat/test_deconvolution_mouse.R b/tests/testthat/test_deconvolution_mouse.R
index 36f487d..c3bcec2 100644
--- a/tests/testthat/test_deconvolution_mouse.R
+++ b/tests/testthat/test_deconvolution_mouse.R
@@ -40,12 +40,12 @@ test_that("generic deconvolution works for all methods", {
 })
 
 test_that("mouse gene names can be converted into their human orthologus, and vice versa", {
-  test_mat_newGenes = convert_human_mouse_genes(test_mat[1:1000, ], convert_to = 'human')
+  test_mat_newGenes <- convert_human_mouse_genes(test_mat[1:1000, ], convert_to = "human")
   assert("matrix dimensions consistent", ncol(test_mat_newGenes) == ncol(test_mat))
 
   test_mat_human <- read_tsv("bulk_mat.tsv") %>%
     as.data.frame() %>%
     tibble::column_to_rownames("gene_symbol")
-  test_mat_newGenes = convert_human_mouse_genes(test_mat_human[1:1000, ], convert_to = 'mouse')
+  test_mat_newGenes <- convert_human_mouse_genes(test_mat_human[1:1000, ], convert_to = "mouse")
   assert("matrix dimensions consistent", ncol(test_mat_newGenes) == ncol(test_mat))
 })

From e9af77051c1f278ecb8f8508951aa3ca503b0a3d Mon Sep 17 00:00:00 2001
From: LorenzoMerotto <LorenzoMerotto@users.noreply.github.com>
Date: Fri, 3 Nov 2023 14:45:48 +0000
Subject: [PATCH 2/2] Roxygenize

---
 man/convert_human_mouse_genes.Rd | 7 -------
 1 file changed, 7 deletions(-)

diff --git a/man/convert_human_mouse_genes.Rd b/man/convert_human_mouse_genes.Rd
index 964d5e8..2ee672c 100644
--- a/man/convert_human_mouse_genes.Rd
+++ b/man/convert_human_mouse_genes.Rd
@@ -4,18 +4,11 @@
 \alias{convert_human_mouse_genes}
 \title{This function converts the mouse gene symbols into corresponding human ones, and vice versa.}
 \usage{
-<<<<<<< HEAD:man/convert_human_mouse_genes.Rd
 convert_human_mouse_genes(
   gene_expression_matrix,
   mirror = "www",
   other_annot = TRUE,
   convert_to = c("human", "mouse")
-=======
-mouse_genes_to_human(
-  gene_expression_matrix,
-  mirror = "www",
-  other_annot = TRUE
->>>>>>> a7e4ee9993aa94f268e862263eaf226a251514f9:man/mouse_genes_to_human.Rd
 )
 }
 \arguments{