rename feature_symbol to feature_name

R/OmicSigFromDifexp.R

@@ -17,7 +17,7 @@
 OmicSigFromDifexp <- function(difexp, metadata, criteria = NULL) {
   ## define the following to pass R check since they are viewed as variables in dplyr functions
   probe_id <- NULL
-  feature_symbol <- NULL
+  feature_name <- NULL
   score <- NULL
   direction <- NULL
 
@@ -53,25 +53,25 @@ OmicSigFromDifexp <- function(difexp, metadata, criteria = NULL) {
   if ("score" %in% colnames(difexp)) {
     if (signatureType %in% c("bi-directional", "categorical")) {
       signatures <- signatures %>%
-        dplyr::select(probe_id, feature_symbol, score, direction) %>%
+        dplyr::select(probe_id, feature_name, score, direction) %>%
         dplyr::arrange(dplyr::desc(abs(score)))
     } else {
       signatures <- signatures %>%
-        dplyr::select(probe_id, feature_symbol, score)
+        dplyr::select(probe_id, feature_name, score)
     }
   } else {
     if (signatureType %in% c("bi-directional", "categorical")) {
       signatures <- signatures %>%
-        dplyr::select(probe_id, feature_symbol, direction)
+        dplyr::select(probe_id, feature_name, direction)
     } else {
       signatures <- signatures %>%
-        dplyr::select(probe_id, feature_symbol)
+        dplyr::select(probe_id, feature_name)
     }
   }
 
   signatures <- signatures %>%
-    dplyr::distinct(feature_symbol, .keep_all = TRUE) %>%
-    filter(feature_symbol != "", complete.cases(.))
+    dplyr::distinct(feature_name, .keep_all = TRUE) %>%
+    filter(feature_name != "", complete.cases(.))
 
   OmicSig <- OmicSignature$new(
     metadata = metadata,

R/OmicSignature.R

@@ -15,7 +15,7 @@ OmicSignature <-
       #' @description
       #' Create a new OmicSignature object
       #' @param metadata required. a list. See `createMetadata` for more information
-      #' @param signature required. a vector, or a dataframe including columns: "probe_id", "feature_symbol" and "direction", and an optional column "score"
+      #' @param signature required. a vector, or a dataframe including columns: "probe_id", "feature_name" and "direction", and an optional column "score"
       #' @param difexp optional
       #' @param print_message use TRUE if want to see all messages printed
       #' @export
@@ -31,10 +31,10 @@ OmicSignature <-
               paste(head(setdiff(signature$probe_id, difexp$probe_id)), collapse = " ")
             ))
           }
-          if (!all(signature$feature_symbol %in% difexp$feature_symbol)) {
+          if (!all(signature$feature_name %in% difexp$feature_name)) {
             stop(paste(
-              "Some features in signature$feature_symbol are not included in difexp$feature_symbol. Examples:",
-              paste(head(setdiff(signature$feature_symbol, difexp$feature_symbol)), collapse = " ")
+              "Some features in signature$feature_name are not included in difexp$feature_name. Examples:",
+              paste(head(setdiff(signature$feature_name, difexp$feature_name)), collapse = " ")
             ))
           }
         }
@@ -89,35 +89,35 @@ OmicSignature <-
         if ("score" %in% colnames(difexp)) {
           if (direction_type == "uni-directional") {
             res <- res %>%
-              dplyr::select(probe_id, feature_symbol, score) %>%
+              dplyr::select(probe_id, feature_name, score) %>%
               dplyr::filter(score != "") %>%
               dplyr::arrange(desc(abs(score)))
           } else if (direction_type == "bi-directional") {
             res <- res %>%
-              dplyr::select(probe_id, feature_symbol, score) %>%
+              dplyr::select(probe_id, feature_name, score) %>%
               dplyr::filter(score != "") %>%
               dplyr::mutate(direction = ifelse(score < 0, "-", "+")) %>%
               dplyr::arrange(desc(abs(score)))
           } else if (direction_type == "categorical") {
             res <- res %>%
-              dplyr::select(probe_id, feature_symbol, score, direction) %>%
+              dplyr::select(probe_id, feature_name, score, direction) %>%
               dplyr::filter(score != "", ) %>%
               dplyr::arrange(desc(abs(score)))
           }
         } else {
           if (direction_type == "uni-directional") {
             res <- res %>%
-              dplyr::select(probe_id, feature_symbol)
+              dplyr::select(probe_id, feature_name)
           } else {
             res <- res %>%
               dplyr::filter(!!!v) %>%
-              dplyr::select(probe_id, feature_symbol, direction)
+              dplyr::select(probe_id, feature_name, direction)
           }
         }
 
         res <- res %>%
-          dplyr::filter(feature_symbol != "", complete.cases(.)) %>%
-          dplyr::distinct(feature_symbol, .keep_all = TRUE) %>%
+          dplyr::filter(feature_name != "", complete.cases(.)) %>%
+          dplyr::distinct(feature_name, .keep_all = TRUE) %>%
           dplyr::mutate(direction = as.character(direction))
 
         return(res)
@@ -134,7 +134,7 @@ OmicSignature <-
           private$.metadata <- private$checkMetadata(value, print_message)
         }
       },
-      #' @field signature a dataframe contains probe_id, feature_symbol, score (optional) and direction (optional)
+      #' @field signature a dataframe contains probe_id, feature_name, score (optional) and direction (optional)
       signature = function(value, print_message = FALSE) {
         if (missing(value)) {
           private$.signature
@@ -186,7 +186,7 @@ OmicSignature <-
         ## require any of p_value, q_value, or adj_p
         exist_p_columns <- intersect(colnames(difexp), c("p_value", "q_value", "adj_p"))
         if (length(exist_p_columns) > 0) {
-          difexpColRequired <- c("probe_id", "feature_symbol", exist_p_columns)
+          difexpColRequired <- c("probe_id", "feature_name", exist_p_columns)
         } else {
           stop("difexp requires at least one of the following columns: p_value, q_value, adj_p.")
         }
@@ -208,10 +208,10 @@ OmicSignature <-
             }
           }
         }
-        ## "feature_symbol" should be character
-        if ("feature_symbol" %in% colnames(difexp)) {
-          if (!is(difexp$feature_symbol, "character")) {
-            stop("difexp: feature_symbol is not character.")
+        ## "feature_name" should be character
+        if ("feature_name" %in% colnames(difexp)) {
+          if (!is(difexp$feature_name, "character")) {
+            stop("difexp: feature_name is not character.")
           }
         }
         private$verbose(v, "  [Success] difexp is valid. \n")
@@ -320,7 +320,7 @@ OmicSignature <-
         signature <- standardizeSigDF(signature)
 
         ## check column names
-        signatureColRequired <- c("probe_id", "feature_symbol")
+        signatureColRequired <- c("probe_id", "feature_name")
         if (signatureType != "uni-directional") {
           signatureColRequired <- c(signatureColRequired, "direction")
         }

R/readwriteJson.R

@@ -66,7 +66,7 @@ readJson <- function(filename) {
   }
 
   #### sig df ####
-  readSignature <- data.frame("probe_id" = readJson$sig_probe_id, "feature_symbol" = readJson$sig_feature_symbol)
+  readSignature <- data.frame("probe_id" = readJson$sig_probe_id, "feature_name" = readJson$sig_feature_name)
   if (!is.null(readJson$sig_score)) {
     readSignature$score <- readJson$sig_score
   }

R/replaceDifexpCol.R

@@ -29,7 +29,7 @@ replaceDifexpCol <- function(colname) {
       "adj.p.val" = "adj_p", "adj.p.value" = "adj_p", "adj.p" = "adj_p", "fdr" = "adj_p",
       "q.value" = "q_value", "qval" = "q_value"
     )
-  colnameMissing <- setdiff(c("id", "symbol", "score"), colname)
+  colnameMissing <- setdiff(c("probe_id", "feature_name", "score"), colname)
   if (length(colnameMissing) > 0) {
     warning(
       "Required column for OmicSignature object difexp: ", paste(colnameMissing, collapse = ", "),

R/signatureVecToDF.R

@@ -1,8 +1,8 @@
 #' @title change a signature vector into a dataframe to be saved into OmicSignature object
 #' updated 10/2024
-#' @param input a character vector of the symbol of the signature, or a numeric vector which names are signature symbols and values are scores.
+#' @param input a character vector of the significant feature names, or a numeric vector which names are feature names and values are scores.
 #' @param bi_directional logical.
-#' @return signature dataframe with columns "feature_symbol", along with "score" and "direction" if applicable
+#' @return signature dataframe with columns "feature_name", along with "score" and "direction" if applicable
 #' @examples
 #' signatures <- c("gene1", "gene2", "gene3")
 #' signatureVecToDF(signatures)
@@ -16,7 +16,7 @@ signatureVecToDF <- function(input, bi_directional = FALSE) {
   if (is.numeric(input) & !is.null(names(input))) {
     DF <- data.frame(
       "probe_id" = seq(length(input)),
-      "feature_symbol" = names(input),
+      "feature_name" = names(input),
       "score" = input
     )
     if (bi_directional) {
@@ -28,7 +28,7 @@ signatureVecToDF <- function(input, bi_directional = FALSE) {
   } else if (is.character(input) | is.factor(input)) {
     DF <- data.frame(
       "probe_id" = seq(length(input)),
-      "feature_symbol" = as.character(input)
+      "feature_name" = as.character(input)
     )
   } else {
     stop("input signature vector is not valid. See `signatureVecToDF()`. ")

R/standardizeSigDF.R

@@ -9,10 +9,10 @@
 #' @export
 standardizeSigDF <- function(sigdf) {
   sigdf <- sigdf %>%
-    dplyr::filter(feature_symbol != "") %>%
+    dplyr::filter(feature_name != "") %>%
     dplyr::mutate(
       probe_id = as.character(probe_id),
-      feature_symbol = as.character(feature_symbol)
+      feature_name = as.character(feature_name)
     )
   if ("score" %in% colnames(sigdf)) {
     sigdf <- sigdf %>%

inst/extdata/OmS_example_1.json

@@ -11,12 +11,12 @@
   "signature_name": ["Experiment in liver"],
   "metadata_length": [10],
   "sig_probe_id": [2, 46, 13, 48, 6, 47, 30, 9, 45, 17, 38, 42, 1, 21, 43, 35, 26, 19],
-  "sig_feature_symbol": ["gene2", "gene46", "gene13", "gene48", "gene6", "gene47", "gene30", "gene9", "gene45", "gene17", "gene38", "gene42", "gene1", "gene21", "gene43", "gene35", "gene26", "gene19"],
+  "sig_feature_name": ["gene2", "gene46", "gene13", "gene48", "gene6", "gene47", "gene30", "gene9", "gene45", "gene17", "gene38", "gene42", "gene1", "gene21", "gene43", "gene35", "gene26", "gene19"],
   "sig_score": [4.99, -4.71, 4.68, -4.67, 4.35, -4.13, 4.09, 3.98, 3.96, -3.94, 3.74, 3.73, 3.69, 3.54, 3.51, 3.37, 3.28, -3.08],
   "sig_direction": ["+", "-", "+", "-", "+", "-", "+", "+", "+", "-", "+", "+", "+", "+", "+", "+", "+", "-"],
-  "difexp_colnames": ["difexp_probe_id", "difexp_feature_symbol", "difexp_score", "difexp_p_value"],
+  "difexp_colnames": ["difexp_probe_id", "difexp_feature_name", "difexp_score", "difexp_p_value"],
   "difexp_probe_id": [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50],
-  "difexp_feature_symbol": ["gene1", "gene2", "gene3", "gene4", "gene5", "gene6", "gene7", "gene8", "gene9", "gene10", "gene11", "gene12", "gene13", "gene14", "gene15", "gene16", "gene17", "gene18", "gene19", "gene20", "gene21", "gene22", "gene23", "gene24", "gene25", "gene26", "gene27", "gene28", "gene29", "gene30", "gene31", "gene32", "gene33", "gene34", "gene35", "gene36", "gene37", "gene38", "gene39", "gene40", "gene41", "gene42", "gene43", "gene44", "gene45", "gene46", "gene47", "gene48", "gene49", "gene50"],
+  "difexp_feature_name": ["gene1", "gene2", "gene3", "gene4", "gene5", "gene6", "gene7", "gene8", "gene9", "gene10", "gene11", "gene12", "gene13", "gene14", "gene15", "gene16", "gene17", "gene18", "gene19", "gene20", "gene21", "gene22", "gene23", "gene24", "gene25", "gene26", "gene27", "gene28", "gene29", "gene30", "gene31", "gene32", "gene33", "gene34", "gene35", "gene36", "gene37", "gene38", "gene39", "gene40", "gene41", "gene42", "gene43", "gene44", "gene45", "gene46", "gene47", "gene48", "gene49", "gene50"],
   "difexp_score": [3.69, 4.99, -1.36, -0.31, -2.13, 4.35, -2.63, 2.22, 3.98, -1.6, 1.38, 2.57, 4.68, 2.44, -1.03, 1.28, -3.94, 1.09, -3.08, -0.4, 3.54, 0.02, 1.41, 1.75, 1.34, 3.28, 0.31, 0.07, -0.22, 4.09, -1.92, 0.7, -0.49, 1.13, 3.37, -0.24, 1.05, 3.74, -0.98, -2.64, 2.98, 3.73, 3.51, -2.17, 3.96, -4.71, -4.13, -4.67, 0.72, -2.4],
   "difexp_p_value": [0.001, 0.029, 0.001, 0.002, 0.002, 0.001, 0.002, 0.009, 0.003, 0.026, 0.001, 0.002, 0.001, 0.001, 0.003, 0.003, 0.001, 0.004, 0.001, 0.004, 0.002, 0.003, 0.001, 0.018, 0.02, 0.011, 0.007, 0.001, 0.001, 0.012, 0.003, 0.001, 0.008, 0.001, 0.004, 0.001, 0.003, 0.002, 0.004, 0.002, 0.007, 0.002, 0.005, 0.001, 0.003, 0.002, 0.001, 0.002, 0.001, 0.001]
 }

inst/extdata/OmS_example_2.json

@@ -11,12 +11,12 @@
   "signature_name": ["Experiment in brain"],
   "metadata_length": [10],
   "sig_probe_id": [14, 9, 15, 25, 16, 2, 50, 27, 41, 33, 20, 43, 49, 1, 17, 48, 8, 7, 22, 31, 34, 30], 
-  "sig_feature_symbol": ["gene14", "gene9", "gene15", "gene25", "gene16", "gene2", "gene50", "gene27", "gene41", "gene33", "gene20", "gene43", "gene49", "gene1", "gene17", "gene48", "gene8", "gene7", "gene22", "gene31", "gene34", "gene30"],
+  "sig_feature_name": ["gene14", "gene9", "gene15", "gene25", "gene16", "gene2", "gene50", "gene27", "gene41", "gene33", "gene20", "gene43", "gene49", "gene1", "gene17", "gene48", "gene8", "gene7", "gene22", "gene31", "gene34", "gene30"],
   "sig_score": [-4.99, -4.86, -4.77, -4.62, -4.59, 4.48, -4.44, -4.17, 4.13, -4.11, -4, 3.78, 3.49, 3.45, -3.42, -3.3, -3.28, -3.27, -3.2, -3.05, -3.04, -3.03],
   "sig_direction": ["-", "-", "-", "-", "-", "+", "-", "-", "+", "-", "-", "+", "+", "+", "-", "-", "-", "-", "-", "-", "-", "-"],
-  "difexp_colnames": ["difexp_probe_id", "difexp_feature_symbol", "difexp_score", "difexp_p_value"],
+  "difexp_colnames": ["difexp_probe_id", "difexp_feature_name", "difexp_score", "difexp_p_value"],
   "difexp_probe_id": [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50],
-  "difexp_feature_symbol": ["gene1", "gene2", "gene3", "gene4", "gene5", "gene6", "gene7", "gene8", "gene9", "gene10", "gene11", "gene12", "gene13", "gene14", "gene15", "gene16", "gene17", "gene18", "gene19", "gene20", "gene21", "gene22", "gene23", "gene24", "gene25", "gene26", "gene27", "gene28", "gene29", "gene30", "gene31", "gene32", "gene33", "gene34", "gene35", "gene36", "gene37", "gene38", "gene39", "gene40", "gene41", "gene42", "gene43", "gene44", "gene45", "gene46", "gene47", "gene48", "gene49", "gene50"],
+  "difexp_feature_name": ["gene1", "gene2", "gene3", "gene4", "gene5", "gene6", "gene7", "gene8", "gene9", "gene10", "gene11", "gene12", "gene13", "gene14", "gene15", "gene16", "gene17", "gene18", "gene19", "gene20", "gene21", "gene22", "gene23", "gene24", "gene25", "gene26", "gene27", "gene28", "gene29", "gene30", "gene31", "gene32", "gene33", "gene34", "gene35", "gene36", "gene37", "gene38", "gene39", "gene40", "gene41", "gene42", "gene43", "gene44", "gene45", "gene46", "gene47", "gene48", "gene49", "gene50"],
   "difexp_score": [3.45, 4.48, -1.95, -2.49, -0.64, 1.47, -3.27, -3.28, -4.86, -0.65, -0.04, -0.49, -0.21, -4.99, -4.77, -4.59, -3.42, 2.47, 2.84, -4, 1.28, -3.2, 2.35, 0.5, -4.62, -0.03, -4.17, 0.17, -1.45, -3.03, -3.05, -2.37, -4.11, -3.04, -2.03, 1.67, 0.36, 1.78, -2.76, -2.58, 4.13, 1.86, 3.78, -1.92, 2.65, 2.85, 1.37, -3.3, 3.49, -4.44],
   "difexp_p_value": [0.004, 0.001, 0.002, 0.003, 0.005, 0.001, 0.001, 0.002, 0.003, 0.01, 0.002, 0.002, 0.001, 0.002, 0.003, 0.005, 0.002, 0.001, 0.001, 0.001, 0.004, 0.001, 0.067, 0.005, 0.001, 0.001, 0.003, 0.001, 0.001, 0.001, 0.001, 0.011, 0.001, 0.003, 0.002, 0.016, 0.002, 0.001, 0.001, 0.05, 0.002, 0.002, 0.002, 0.01, 0.001, 0.001, 0.002, 0.004, 0.002, 0.002]
 }

inst/extdata/OmS_example_3.json

@@ -11,12 +11,12 @@
   "signature_name": ["Experiment in heart"],
   "metadata_length": [10],
   "sig_probe_id": [28, 32, 25, 49, 6, 38, 43, 27, 46, 39, 11, 29, 15, 2, 14, 4, 9, 45, 24, 33, 47, 16, 10, 7],
-  "sig_feature_symbol": ["gene28", "gene32", "gene25", "gene49", "gene6", "gene38", "gene43", "gene27", "gene46", "gene39", "gene11", "gene29", "gene15", "gene2", "gene14", "gene4", "gene9", "gene45", "gene24", "gene33", "gene47", "gene16", "gene10", "gene7"],
+  "sig_feature_name": ["gene28", "gene32", "gene25", "gene49", "gene6", "gene38", "gene43", "gene27", "gene46", "gene39", "gene11", "gene29", "gene15", "gene2", "gene14", "gene4", "gene9", "gene45", "gene24", "gene33", "gene47", "gene16", "gene10", "gene7"],
   "sig_score": [4.99, -4.9, 4.71, -4.7, -4.54, -4.44, 4.4, -4.1, 4.09, -4.04, 3.92, 3.88, -3.84, 3.79, 3.72, 3.65, -3.61, -3.42, 3.4, -3.28, -3.16, -3.15, -3.1, -3.03],
   "sig_direction": ["+", "-", "+", "-", "-", "-", "+", "-", "+", "-", "+", "+", "-", "+", "+", "+", "-", "-", "+", "-", "-", "-", "-", "-"],
-  "difexp_colnames": ["difexp_probe_id", "difexp_feature_symbol", "difexp_score", "difexp_p_value"],
+  "difexp_colnames": ["difexp_probe_id", "difexp_feature_name", "difexp_score", "difexp_p_value"],
   "difexp_probe_id": [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50],
-  "difexp_feature_symbol": ["gene1", "gene2", "gene3", "gene4", "gene5", "gene6", "gene7", "gene8", "gene9", "gene10", "gene11", "gene12", "gene13", "gene14", "gene15", "gene16", "gene17", "gene18", "gene19", "gene20", "gene21", "gene22", "gene23", "gene24", "gene25", "gene26", "gene27", "gene28", "gene29", "gene30", "gene31", "gene32", "gene33", "gene34", "gene35", "gene36", "gene37", "gene38", "gene39", "gene40", "gene41", "gene42", "gene43", "gene44", "gene45", "gene46", "gene47", "gene48", "gene49", "gene50"],
+  "difexp_feature_name": ["gene1", "gene2", "gene3", "gene4", "gene5", "gene6", "gene7", "gene8", "gene9", "gene10", "gene11", "gene12", "gene13", "gene14", "gene15", "gene16", "gene17", "gene18", "gene19", "gene20", "gene21", "gene22", "gene23", "gene24", "gene25", "gene26", "gene27", "gene28", "gene29", "gene30", "gene31", "gene32", "gene33", "gene34", "gene35", "gene36", "gene37", "gene38", "gene39", "gene40", "gene41", "gene42", "gene43", "gene44", "gene45", "gene46", "gene47", "gene48", "gene49", "gene50"],
   "difexp_score": [1.96, 3.79, 2.9, 3.65, 2.1, -4.54, -3.03, -0.22, -3.61, -3.1, 3.92, -0.55, -2.98, 3.72, -3.84, -3.15, 0.21, -0.17, -0.91, 0.57, 0.6, 0.94, 2.12, 3.4, 4.71, 1.99, -4.1, 4.99, 3.88, 2.05, 2.38, -4.9, -3.28, -2.21, -2.22, -2.99, 1.92, -4.44, -4.04, 0.15, -2.97, 0.53, 4.4, -1.82, -3.42, 4.09, -3.16, -2.63, -4.7, 1],
   "difexp_p_value": [0.001, 0.003, 0.002, 0.002, 0.001, 0.001, 0.026, 0.002, 0.002, 0.006, 0.005, 0.001, 0.005, 0.001, 0.001, 0.001, 0.006, 0.003, 0.002, 0.002, 0.001, 0.25, 0.003, 0.001, 0.001, 0.001, 0.004, 0.007, 0.002, 0.004, 0.091, 0.001, 0.001, 0.001, 0.001, 0.001, 0.001, 0.001, 0.002, 0.002, 0.003, 0.012, 0.02, 0.002, 0.002, 0.002, 0.006, 0.002, 0.002, 0.002]
 }