Added checks.

Added checks of valid domains/species for scoreWTSequences.

Author: kvnkuang

R/Rmimp.R

@@ -6,7 +6,7 @@ library(GenomicRanges)
 library(data.table)
 library(Biostrings)
 
-if(F){
+if(T){
   setwd('~/Desktop/Repos/rmimp/')
   BASE_DIR = '~/Desktop/Repos/rmimp/inst/extdata'
   source('R/display-functions.r')
@@ -485,6 +485,22 @@ pRewiringPosterior <- function(wt.scores, mt.scores, fg.params, bg.params, auc=1
 #' @import data.table
 #' @export
 scoreWTSequence <- function(wt_seqs, central = T, domain = "phos", species = "human", model.data = "hconf", cores = 2) {
+  # Ensure valid domain
+  if (central) {
+    valid.domains <- .VALID_DOMAINS$central
+  } else {
+    valid.domains <- .VALID_DOMAINS$not_central
+  }
+  
+  if (!is.element(domain, valid.domains)) {
+    stop("Domain must be valid. Please check MIMP documentation for a list of valid domains")
+  }
+  
+  # Ensure valid species
+  if (!is.element(species, .VALID_SPECIES[[domain]])) {
+    stop("Species must be valid. Please check MIMP documentation for a list of valid domains")
+  }
+  
   # Load model
   cat('\r.... | loading specificity models')
   mpath <- .getModelDataPath(model.data, domain = domain, species = species)

R/display-functions.r

@@ -9,8 +9,7 @@
 #'
 #' @param s Data frame resulting from mimp call.
 #' @param dist Distance of mutation.
-#'
-#' @keywords helper mimp
+#' @noRd
 .htmlSeq <- function(s, dist) {
   s = strsplit(s, '')[[1]]
   if (dist != 0)
@@ -26,8 +25,7 @@
 #'
 #' @param s Data frame resulting from mimp call.
 #' @param dist Distance of mutation.
-#'
-#' @keywords helper mimp
+#' @noRd
 .htmlSeqSh3 <- function(wt, mut) {
   wtSplit <- strsplit(wt, '')[[1]]
   mutSplit <- strsplit(mut, '')[[1]]
@@ -48,8 +46,6 @@
 #' @param HL_DIR Directory containing overlays
 #' @param logoExt Extension of logo files
 #' @param .webserver Request coming from webserver?
-#'
-#' @keywords display mimp
 dohtml <- function(x, LOGO_DIR, HL_DIR, logoExt = ".svg", .webserver = F) {
   x = unfactor(x)
   x$score_wt = signif(x$score_wt, 3)
@@ -151,8 +147,6 @@ dohtml <- function(x, LOGO_DIR, HL_DIR, logoExt = ".svg", .webserver = F) {
 #' @param HL_DIR Directory containing overlays
 #' @param logoExt Extension of logo files
 #' @param .webserver Request coming from webserver?
-#'
-#' @keywords display mimp
 dohtmlSh3 <- function(x, LOGO_DIR, HL_DIR, logoExt = ".svg", .webserver = F) {
   x = unfactor(x)
   x$score_wt = signif(x$score_wt, 3)

R/pwm-functions.r

@@ -201,10 +201,7 @@ scoreArrayRolling <- function(seqs, pwm){
 #'
 #' @param seqs Sequences to be scored
 #' @param pwm Position weight matrix
-#'  
-#' @keywords pwm mss match tfbs
-#' @examples
-#' # No Examples
+#' @noRd
 .mssNonCentral <- function(seqs, pwm){
   # Best/worst sequence match
   oa = scoreArrayFast(bestSequence(pwm), pwm, do_sum = F)[[1]]