build: update renv and dependencies

Author: AliSajid

.Rbuildignore

@@ -18,6 +18,7 @@
 ^\.vale\.ini$
 ^\.vscode$
 ^_pkgdown\.yml$
+^codecov\.yaml$
 ^codecov\.yml$
 ^codemeta\.json$
 ^data-raw$

.pre-commit-config.yaml

@@ -3,7 +3,7 @@
 exclude: '.*\.(csv|tsv|xls)$'
 repos:
   - repo: https://github.com/lorenzwalthert/precommit
-    rev: v0.4.3.9017
+    rev: v0.4.3.9020
     hooks:
       - id: use-tidy-description
       - id: codemeta-description-updated

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: drugfindR
 Title: Investigate iLINCS for candidate repurposable drugs
-Version: 0.99.1363
+Version: 0.99.1364
 Authors@R: c(
     person(given = c("Ali", "Sajid"),
            family = "Imami",

R/consensusConcordants.R

@@ -427,10 +427,11 @@ NULL
 #' }
 #'
 consensusConcordants <- function(
-    ...,
-    paired = FALSE,
-    cutoff = 0.321,
-    cellLine = NULL) {
+  ...,
+  paired = FALSE,
+  cutoff = 0.321,
+  cellLine = NULL
+) {
     # Capture input dataframes
     dots <- list(...)
 

R/filterSignature.R

@@ -469,8 +469,9 @@
 #' # Get top 20% most up-regulated genes
 #' topUpregulated <- filterSignature(kdSignature, direction = "up", prop = 0.2)
 filterSignature <- function(
-    signature, direction = "any",
-    threshold = NULL, prop = NULL) {
+  signature, direction = "any",
+  threshold = NULL, prop = NULL
+) {
     # Validate input parameters
     .validateFilterSignatureInput(signature, direction, threshold, prop)
 

R/investigateSignature.R

@@ -74,20 +74,21 @@ NULL
 #' head(investigatedSignature)
 #' }
 investigateSignature <- function(
-    expr,
-    outputLib,
-    filterThreshold = NULL,
-    filterProp = NULL,
-    similarityThreshold = 0.2,
-    paired = TRUE,
-    outputCellLines = NULL,
-    geneColumn = "Symbol",
-    logfcColumn = "logFC",
-    pvalColumn = "PValue",
-    sourceName = "Input",
-    sourceCellLine = NA,
-    sourceTime = NA,
-    sourceConcentration = NA) {
+  expr,
+  outputLib,
+  filterThreshold = NULL,
+  filterProp = NULL,
+  similarityThreshold = 0.2,
+  paired = TRUE,
+  outputCellLines = NULL,
+  geneColumn = "Symbol",
+  logfcColumn = "logFC",
+  pvalColumn = "PValue",
+  sourceName = "Input",
+  sourceCellLine = NA,
+  sourceTime = NA,
+  sourceConcentration = NA
+) {
     stopIfInvalidLibraries(outputLib) # nolint: object_usage_linter.
     if (missing(outputLib)) {
         stop("Please specify an output library", call. = FALSE)

R/investigateTarget.R

@@ -129,12 +129,13 @@ NULL
 #' # })
 #' }
 investigateTarget <- function(
-    target,
-    inputLib, outputLib,
-    filterThreshold = 0.85,
-    similarityThreshold = 0.321,
-    paired = TRUE, inputCellLines = NULL,
-    outputCellLines = NULL) {
+  target,
+  inputLib, outputLib,
+  filterThreshold = 0.85,
+  similarityThreshold = 0.321,
+  paired = TRUE, inputCellLines = NULL,
+  outputCellLines = NULL
+) {
     stopIfInvalidLibraries(c(inputLib, outputLib)) # nolint: object_usage_linter.
 
     # Load metadata and obtain candidate source signatures for the target

R/prepareSignature.R

@@ -247,9 +247,10 @@
 #' )
 #' print(custom_signature)
 prepareSignature <- function(
-    dge, geneColumn = "Symbol",
-    logfcColumn = "logFC",
-    pvalColumn = "PValue") {
+  dge, geneColumn = "Symbol",
+  logfcColumn = "logFC",
+  pvalColumn = "PValue"
+) {
     # Validate input parameters
     .validatePrepareSignatureInput(dge, geneColumn, logfcColumn, pvalColumn)
 

R/utilities.R

@@ -434,13 +434,14 @@ stopIfInvalidSignature <- function(signature) {
 #'
 #' @examples NULL
 .computeConsensusFromSignature <- function(
-    signature,
-    outputLib,
-    filterThreshold = NULL,
-    filterProp = NULL,
-    similarityThreshold = 0.321,
-    paired = TRUE,
-    outputCellLines = NULL) {
+  signature,
+  outputLib,
+  filterThreshold = NULL,
+  filterProp = NULL,
+  similarityThreshold = 0.321,
+  paired = TRUE,
+  outputCellLines = NULL
+) {
     stopIfInvalidLibraries(outputLib)
 
     if (paired) {

README.Rmd

@@ -182,7 +182,7 @@ If you use drugfindR in your research, please cite:
 ```
 Imami AS, Sahay S, Creeden JF, McCullumsmith RE (2024).
 drugfindR: Investigate iLINCS for candidate repurposable drugs.
-R package version 0.99.1363.
+R package version 0.99.1364.
 doi:10.5281/zenodo.338354715
 ```