| ... | ... |
@@ -12,6 +12,8 @@ |
| 12 | 12 |
#' gene symbols representing an edge and any/all other column[s] contain |
| 13 | 13 |
#' corresponding edge data. |
| 14 | 14 |
#' @param data_column_no The column index for desired user data to be added |
| 15 |
+#' @param map_type If the genes in your data set are left untranslated |
|
| 16 |
+#' set to "NUMBER" (assuming numbers are gene accession numbers) |
|
| 15 | 17 |
#' @param only_mapped A logical indicator; if set to FALSE will return 'de-novo' |
| 16 | 18 |
#' edges that 'exist' in data but are not documented in KEGG |
| 17 | 19 |
#' @return A data frame object with detailed KEGG edge mappings annotated with |
| ... | ... |
@@ -30,40 +32,48 @@ |
| 30 | 32 |
#' only_mapped = TRUE) |
| 31 | 33 |
|
| 32 | 34 |
|
| 33 |
-add_edge_data <- function(expanded_edges, KEGG_mappings, |
|
| 34 |
- user_data, data_column_no = 3, only_mapped = FALSE) {
|
|
| 35 |
+add_edge_data <- function(expanded_edges, KEGG_mappings, |
|
| 36 |
+ user_data, map_type = "SYMBOL",data_column_no = 3, |
|
| 37 |
+ only_mapped = FALSE) {
|
|
| 35 | 38 |
|
| 36 | 39 |
expanded_edges <- expanded_edges[expanded_edges$type != "maplink", ] |
| 37 |
- |
|
| 38 |
- # if ("pre_mapped" %in% names(user_data)) {
|
|
| 39 |
- # user_data <- user_data[, -c(which(colnames(user_data) == "pre_mapped"))] |
|
| 40 |
- # } |
|
| 41 |
- |
|
| 42 | 40 |
if (nrow(expanded_edges) > 0) {
|
| 41 |
+ if (map_type == "SYMBOL"){
|
|
| 42 |
+ expanded_edges$unique_ID = |
|
| 43 |
+ paste0(expanded_edges$entry1symbol, ",", |
|
| 44 |
+ expanded_edges$entry2symbol) |
|
| 45 |
+ expanded_edges$unique_IDR = |
|
| 46 |
+ paste0(expanded_edges$entry2symbol, ",", |
|
| 47 |
+ expanded_edges$entry1symbol) |
|
| 48 |
+ } |
|
| 49 |
+ if (map_type == "NUMBER"){
|
|
| 50 |
+ expanded_edges$unique_ID = |
|
| 51 |
+ paste0(expanded_edges$entry1accession, ",", |
|
| 52 |
+ expanded_edges$entry2accession) |
|
| 53 |
+ expanded_edges$unique_IDR = |
|
| 54 |
+ paste0(expanded_edges$entry2accession, ",", |
|
| 55 |
+ expanded_edges$entry1accession) |
|
| 56 |
+ } |
|
| 43 | 57 |
|
| 44 |
- expanded_edges$unique_ID = paste0(expanded_edges$entry1symbol, ",", |
|
| 45 |
- expanded_edges$entry2symbol) |
|
| 46 |
- expanded_edges$unique_IDR = paste0(expanded_edges$entry2symbol, ",", |
|
| 47 |
- expanded_edges$entry1symbol) |
|
| 48 |
- user_data$unique_ID = paste0(user_data$knockout1, ",", |
|
| 49 |
- user_data$knockout2) |
|
| 50 |
- pre_mapped1 <- subset(user_data, user_data$unique_ID %in% |
|
| 51 |
- expanded_edges$unique_ID) |
|
| 52 |
- pre_mapped2 <- subset(user_data, user_data$unique_ID %in% |
|
| 53 |
- expanded_edges$unique_IDR) |
|
| 58 |
+ user_data$unique_ID = paste0(user_data[,1], ",", |
|
| 59 |
+ user_data[,2]) |
|
| 60 |
+ pre_mapped1 <- subset(user_data, user_data$unique_ID %in% |
|
| 61 |
+ expanded_edges$unique_ID) |
|
| 62 |
+ pre_mapped2 <- subset(user_data, user_data$unique_ID %in% |
|
| 63 |
+ expanded_edges$unique_IDR) |
|
| 54 | 64 |
pre_mapped2 <- pre_mapped2[, c(2, 1, 3:ncol(pre_mapped2))] |
| 55 | 65 |
names(pre_mapped2) = names(pre_mapped1) |
| 56 | 66 |
if (nrow(pre_mapped2) >= 1 & nrow(pre_mapped1) >= 1) {
|
| 57 |
- pre_mapped2$unique_ID <- paste0(pre_mapped2$knockout1, ",", |
|
| 58 |
- pre_mapped2$knockout2) |
|
| 67 |
+ pre_mapped2$unique_ID <- paste0(pre_mapped2[,1], ",", |
|
| 68 |
+ pre_mapped2[,2]) |
|
| 59 | 69 |
pre_mapped <- rbind(pre_mapped1, pre_mapped2) |
| 60 | 70 |
} |
| 61 | 71 |
if (nrow(pre_mapped2) == 0 & (nrow(pre_mapped1) == 0)) {
|
| 62 | 72 |
pre_mapped <- data.frame(unique_ID = NA) |
| 63 | 73 |
} |
| 64 | 74 |
if (nrow(pre_mapped1) == 0 & nrow(pre_mapped2) >= 1) {
|
| 65 |
- pre_mapped2$unique_ID <- paste0(pre_mapped2$knockout1, ",", |
|
| 66 |
- pre_mapped2$knockout2) |
|
| 75 |
+ pre_mapped2$unique_ID <- paste0(pre_mapped2[,1], ",", |
|
| 76 |
+ pre_mapped2[,2]) |
|
| 67 | 77 |
pre_mapped <- pre_mapped2 |
| 68 | 78 |
} |
| 69 | 79 |
if (nrow(pre_mapped2) == 0 & nrow(pre_mapped1) >= 1) {
|
| ... | ... |
@@ -71,72 +81,76 @@ add_edge_data <- function(expanded_edges, KEGG_mappings, |
| 71 | 81 |
} |
| 72 | 82 |
if (!is.na(pre_mapped[1, 1])) {
|
| 73 | 83 |
expanded_edges_1 <- subset(expanded_edges, expanded_edges$unique_ID |
| 74 |
- %in% pre_mapped$unique_ID) |
|
| 75 |
- expanded_edges_1 <- expanded_edges[expanded_edges$unique_ID %in% |
|
| 76 |
- pre_mapped$unique_ID, ] |
|
| 77 |
- expanded_edges_2 <- expanded_edges[!expanded_edges$unique_ID %in% |
|
| 78 |
- pre_mapped$unique_ID, ] |
|
| 84 |
+ %in% pre_mapped$unique_ID) |
|
| 85 |
+ expanded_edges_1 <- expanded_edges[expanded_edges$unique_ID %in% |
|
| 86 |
+ pre_mapped$unique_ID, ] |
|
| 87 |
+ expanded_edges_2 <- expanded_edges[!expanded_edges$unique_ID %in% |
|
| 88 |
+ pre_mapped$unique_ID, ] |
|
| 79 | 89 |
expanded_edges_1$has_data = 1 |
| 80 | 90 |
testval <- nrow(expanded_edges_2) |
| 81 | 91 |
if (testval > 0) {
|
| 82 | 92 |
expanded_edges_2$has_data = 0 |
| 83 | 93 |
edge_set <- rbind(expanded_edges_1, expanded_edges_2) |
| 84 |
- } else {
|
|
| 94 |
+ } |
|
| 95 |
+ else {
|
|
| 85 | 96 |
edge_set <- expanded_edges_1 |
| 86 | 97 |
} |
| 87 |
- |
|
| 98 |
+ |
|
| 88 | 99 |
edge_set <- edge_set[order(edge_set$unique_ID), ] |
| 89 | 100 |
|
| 90 | 101 |
data_to_add <- data.frame("unique_ID" = pre_mapped$unique_ID, stringsAsFactors = FALSE)
|
| 91 | 102 |
data_to_add <- cbind(data_to_add, pre_mapped[, data_column_no]) |
| 92 |
- |
|
| 103 |
+ |
|
| 93 | 104 |
data_to_add <- data_to_add[order(data_to_add$unique_ID), ] |
| 105 |
+ colnames(data_to_add)[2] <- "summary_score" |
|
| 94 | 106 |
|
| 95 |
- annotated_edges <- merge(edge_set, data_to_add, "unique_ID", |
|
| 107 |
+ annotated_edges <- merge(edge_set, data_to_add, "unique_ID", |
|
| 96 | 108 |
all.x = TRUE) |
| 97 | 109 |
drops <- c("unique_ID", "unique_IDR")
|
| 98 |
- annotated_edges <- annotated_edges[, !(names(annotated_edges) %in% |
|
| 99 |
- drops)] |
|
| 100 |
- cat(paste0("Number of edges documented in selected pathway = ",
|
|
| 101 |
- nrow(annotated_edges)), "\n") |
|
| 102 |
- cat(paste0("Number of edges with corresponding user data = ",
|
|
| 103 |
- sum(annotated_edges$has_data), "\n")) |
|
| 110 |
+ annotated_edges <- annotated_edges[, !(names(annotated_edges) %in% |
|
| 111 |
+ drops)] |
|
| 112 |
+ cat(paste0("Number of edges documented in selected pathway = ",
|
|
| 113 |
+ nrow(annotated_edges)), "\n") |
|
| 114 |
+ cat(paste0("Number of edges with corresponding user data = ",
|
|
| 115 |
+ sum(annotated_edges$has_data), "\n")) |
|
| 104 | 116 |
cat(paste0("Coverage = ", round(sum(annotated_edges$has_data)/
|
| 105 |
- nrow(annotated_edges) * 100, 2), "%", "\n")) |
|
| 117 |
+ nrow(annotated_edges) * 100, 2), "%", "\n")) |
|
| 106 | 118 |
annotated_edges$premapped <- 1 |
| 107 |
- un_mapped <- subset(user_data, !user_data$unique_ID %in% |
|
| 108 |
- expanded_edges$unique_ID & |
|
| 109 |
- !user_data$unique_ID %in% expanded_edges$unique_IDR) |
|
| 110 |
- un_mapped_edges <- un_mapped[, c(1:2, data_column_no, |
|
| 111 |
- ncol(un_mapped))] |
|
| 119 |
+ # un_mapped <- subset(user_data, !user_data$unique_ID %in% |
|
| 120 |
+ # expanded_edges$unique_ID & |
|
| 121 |
+ # !user_data$unique_ID %in% expanded_edges$unique_IDR) |
|
| 122 |
+ # un_mapped_edges <- un_mapped[, c(1:2, data_column_no, |
|
| 123 |
+ # ncol(un_mapped))] |
|
| 112 | 124 |
|
| 113 | 125 |
if (only_mapped) {
|
| 114 | 126 |
return(annotated_edges) |
| 115 | 127 |
} |
| 116 |
- } else {
|
|
| 128 |
+ } |
|
| 129 |
+ else {
|
|
| 117 | 130 |
annotated_edges <- expanded_edges |
| 118 | 131 |
annotated_edges$premapped <- 1 |
| 119 | 132 |
annotated_edges$has_data <- 0 |
| 120 | 133 |
un_mapped <- user_data |
| 121 |
- un_mapped$unique_ID <- paste0(un_mapped$knockout1, |
|
| 122 |
- un_mapped$knockout2) |
|
| 123 |
- un_mapped_edges <- un_mapped[, c(1:2, data_column_no, |
|
| 124 |
- ncol(un_mapped))] |
|
| 134 |
+ un_mapped$unique_ID <- paste0(un_mapped$knockout1, |
|
| 135 |
+ un_mapped$knockout2) |
|
| 136 |
+ un_mapped_edges <- un_mapped[, c(1:2, data_column_no, |
|
| 137 |
+ ncol(un_mapped))] |
|
| 125 | 138 |
un_mapped_edges$premapped <- 0 |
| 126 | 139 |
un_mapped_edges$has_data <- 0 |
| 127 |
- cat(paste0("Number of edges documented in selected pathway = ",
|
|
| 128 |
- nrow(annotated_edges)), "\n") |
|
| 129 |
- cat(paste0("Number of edges with corresponding user data = ",
|
|
| 130 |
- sum(annotated_edges$has_data), "\n")) |
|
| 140 |
+ cat(paste0("Number of edges documented in selected pathway = ",
|
|
| 141 |
+ nrow(annotated_edges)), "\n") |
|
| 142 |
+ cat(paste0("Number of edges with corresponding user data = ",
|
|
| 143 |
+ sum(annotated_edges$has_data), "\n")) |
|
| 131 | 144 |
cat(paste0("Coverage = ", round(sum(annotated_edges$has_data)/
|
| 132 |
- nrow(annotated_edges) * 100, 2), "%", "\n")) |
|
| 145 |
+ nrow(annotated_edges) * 100, 2), "%", "\n")) |
|
| 133 | 146 |
if (only_mapped) {
|
| 134 |
- cat(paste0("No documented edges are found in data;
|
|
| 135 |
- only data for de-novo edges can be mapped \n")) |
|
| 147 |
+ cat(paste0("No documented edges are found in data;
|
|
| 148 |
+ only data for de-novo edges can be mapped \n")) |
|
| 136 | 149 |
return(annotated_edges) |
| 137 | 150 |
} |
| 138 | 151 |
} |
| 139 |
- } else if (nrow(expanded_edges) == 0) {
|
|
| 152 |
+ } |
|
| 153 |
+ else if (nrow(expanded_edges) == 0) {
|
|
| 140 | 154 |
annotated_edges <- expanded_edges |
| 141 | 155 |
annotated_edges$premapped <- 1 |
| 142 | 156 |
annotated_edges$has_data <- 0 |
| ... | ... |
@@ -145,24 +159,24 @@ add_edge_data <- function(expanded_edges, KEGG_mappings, |
| 145 | 159 |
un_mapped_edges <- un_mapped[, c(1:2, data_column_no, ncol(un_mapped))] |
| 146 | 160 |
un_mapped_edges$premapped <- 0 |
| 147 | 161 |
un_mapped_edges$has_data <- 0 |
| 148 |
- cat(paste0("Number of edges documented in selected pathway = ",
|
|
| 149 |
- nrow(annotated_edges)), "\n") |
|
| 150 |
- cat(paste0("Number of edges with corresponding user data = ",
|
|
| 151 |
- sum(annotated_edges$has_data), "\n")) |
|
| 162 |
+ cat(paste0("Number of edges documented in selected pathway = ",
|
|
| 163 |
+ nrow(annotated_edges)), "\n") |
|
| 164 |
+ cat(paste0("Number of edges with corresponding user data = ",
|
|
| 165 |
+ sum(annotated_edges$has_data), "\n")) |
|
| 152 | 166 |
cat(paste0("Coverage = ", round(sum(annotated_edges$has_data)/
|
| 153 |
- nrow(annotated_edges) * 100, 2), "%", "\n")) |
|
| 167 |
+ nrow(annotated_edges) * 100, 2), "%", "\n")) |
|
| 154 | 168 |
if (only_mapped) {
|
| 155 | 169 |
return(annotated_edges) |
| 156 | 170 |
} |
| 157 | 171 |
} |
| 158 | 172 |
names(un_mapped_edges)[1:2] <- c("entryNAME_1", "entryNAME_2")
|
| 159 | 173 |
for (i in 1:nrow(un_mapped_edges)) {
|
| 160 |
- un_mapped_edges$Source_eid[i] <- |
|
| 161 |
- list(KEGG_mappings$entryID[which(KEGG_mappings$entrySYMBOL == |
|
| 162 |
- un_mapped_edges$entryNAME_1[i])]) |
|
| 163 |
- un_mapped_edges$Target_eid[i] <- |
|
| 164 |
- list(KEGG_mappings$entryID[which(KEGG_mappings$entrySYMBOL == |
|
| 165 |
- un_mapped_edges$entryNAME_2[i])]) |
|
| 174 |
+ un_mapped_edges$Source_eid[i] <- |
|
| 175 |
+ list(KEGG_mappings$entryID[which(KEGG_mappings$entrySYMBOL == |
|
| 176 |
+ un_mapped_edges$entryNAME_1[i])]) |
|
| 177 |
+ un_mapped_edges$Target_eid[i] <- |
|
| 178 |
+ list(KEGG_mappings$entryID[which(KEGG_mappings$entrySYMBOL == |
|
| 179 |
+ un_mapped_edges$entryNAME_2[i])]) |
|
| 166 | 180 |
x <- length(unlist(un_mapped_edges$Source_eid[i])) |
| 167 | 181 |
y <- length(unlist(un_mapped_edges$Target_eid[i])) |
| 168 | 182 |
if (x > 1 | y > 1) {
|
| ... | ... |
@@ -171,45 +185,45 @@ add_edge_data <- function(expanded_edges, KEGG_mappings, |
| 171 | 185 |
un_mapped_edges$simple[i] <- TRUE |
| 172 | 186 |
} |
| 173 | 187 |
} |
| 174 |
- simple_un_mapped_edges <- un_mapped_edges[un_mapped_edges$simple == TRUE, |
|
| 175 |
- -ncol(un_mapped_edges)] |
|
| 176 |
- complex_un_mapped_edges <- un_mapped_edges[un_mapped_edges$simple == FALSE, |
|
| 177 |
- -ncol(un_mapped_edges)] |
|
| 188 |
+ simple_un_mapped_edges <- un_mapped_edges[un_mapped_edges$simple == TRUE, |
|
| 189 |
+ -ncol(un_mapped_edges)] |
|
| 190 |
+ complex_un_mapped_edges <- un_mapped_edges[un_mapped_edges$simple == FALSE, |
|
| 191 |
+ -ncol(un_mapped_edges)] |
|
| 178 | 192 |
test_val <- nrow(complex_un_mapped_edges) |
| 179 | 193 |
if (test_val == 0) {
|
| 180 | 194 |
un_mapped_edges <- simple_un_mapped_edges |
| 181 | 195 |
} else {
|
| 182 | 196 |
keeps <- c("Source_eid", "Target_eid", "unique_ID")
|
| 183 |
- c_temp <- complex_un_mapped_edges[, (names(complex_un_mapped_edges) %in% |
|
| 184 |
- keeps)] |
|
| 197 |
+ c_temp <- complex_un_mapped_edges[, (names(complex_un_mapped_edges) %in% |
|
| 198 |
+ keeps)] |
|
| 185 | 199 |
|
| 186 | 200 |
for (i in 1:nrow(c_temp)) {
|
| 187 | 201 |
x <- length(unlist(c_temp$Source_eid[i])) |
| 188 | 202 |
y <- length(unlist(c_temp$Target_eid[i])) |
| 189 | 203 |
l <- x * y |
| 190 | 204 |
|
| 191 |
- c_temp$Source_eid[i] <- list(sort(unlist(rep(c_temp$Source_eid[i], |
|
| 192 |
- y)))) |
|
| 205 |
+ c_temp$Source_eid[i] <- list(sort(unlist(rep(c_temp$Source_eid[i], |
|
| 206 |
+ y)))) |
|
| 193 | 207 |
c_temp$Target_eid[i] <- list(unlist(rep(c_temp$Target_eid[i], x))) |
| 194 | 208 |
c_temp$unique_ID[i] <- list(rep(c_temp$unique_ID[i], l)) |
| 195 | 209 |
} |
| 196 | 210 |
|
| 197 |
- c_temp <- data.frame(unique_ID = unlist(c_temp$unique_ID), Source_eid = |
|
| 198 |
- unlist(c_temp$Source_eid), |
|
| 199 |
- Target_eid = unlist(c_temp$Target_eid)) |
|
| 211 |
+ c_temp <- data.frame(unique_ID = unlist(c_temp$unique_ID), Source_eid = |
|
| 212 |
+ unlist(c_temp$Source_eid), |
|
| 213 |
+ Target_eid = unlist(c_temp$Target_eid)) |
|
| 200 | 214 |
drops <- c("Source_eid", "Target_eid")
|
| 201 |
- complex_un_mapped_edges <- |
|
| 202 |
- complex_un_mapped_edges[, !(names(complex_un_mapped_edges) %in% |
|
| 203 |
- drops)] |
|
| 215 |
+ complex_un_mapped_edges <- |
|
| 216 |
+ complex_un_mapped_edges[, !(names(complex_un_mapped_edges) %in% |
|
| 217 |
+ drops)] |
|
| 204 | 218 |
complex_un_mapped_edges <- merge(complex_un_mapped_edges, c_temp) |
| 205 |
- un_mapped_edges <- rbind(simple_un_mapped_edges, |
|
| 219 |
+ un_mapped_edges <- rbind(simple_un_mapped_edges, |
|
| 206 | 220 |
complex_un_mapped_edges) |
| 207 | 221 |
} |
| 208 | 222 |
un_mapped_edges$Source_eid <- unlist(un_mapped_edges$Source_eid) |
| 209 | 223 |
un_mapped_edges$Target_eid <- unlist(un_mapped_edges$Target_eid) |
| 210 |
- un_mapped_edges <- plyr::rename(un_mapped_edges, c(Source_eid = "entry1", |
|
| 211 |
- Target_eid = "entry2", entryNAME_1 = "entry1symbol", |
|
| 212 |
- entryNAME_2 = "entry2symbol")) |
|
| 224 |
+ un_mapped_edges <- plyr::rename(un_mapped_edges, c(Source_eid = "entry1", |
|
| 225 |
+ Target_eid = "entry2", entryNAME_1 = "entry1symbol", |
|
| 226 |
+ entryNAME_2 = "entry2symbol")) |
|
| 213 | 227 |
un_mapped_edges$subtype1 <- "de_novo" |
| 214 | 228 |
|
| 215 | 229 |
drops <- c("unique_ID")
|
| ... | ... |
@@ -217,38 +231,38 @@ add_edge_data <- function(expanded_edges, KEGG_mappings, |
| 217 | 231 |
un_mapped_edges$has_data <- 1 |
| 218 | 232 |
un_mapped_edges$premapped <- 0 |
| 219 | 233 |
for (i in 1:nrow(un_mapped_edges)) {
|
| 220 |
- un_mapped_edges$entry1accession[i] <- |
|
| 221 |
- KEGG_mappings$entryACCESSION[which(KEGG_mappings$entrySYMBOL == |
|
| 222 |
- un_mapped_edges$entry1symbol[i])][1] |
|
| 223 |
- un_mapped_edges$entry2accession[i] <- |
|
| 224 |
- KEGG_mappings$entryACCESSION[which(KEGG_mappings$entrySYMBOL == |
|
| 225 |
- un_mapped_edges$entry2symbol[i])][1] |
|
| 226 |
- un_mapped_edges$entry1type[i] <- |
|
| 227 |
- KEGG_mappings$entryTYPE[which(KEGG_mappings$entrySYMBOL == |
|
| 228 |
- un_mapped_edges$entry1symbol[i])][1] |
|
| 229 |
- un_mapped_edges$entry2type[i] <- |
|
| 230 |
- KEGG_mappings$entryTYPE[which(KEGG_mappings$entrySYMBOL == |
|
| 231 |
- un_mapped_edges$entry2symbol[i])][1] |
|
| 234 |
+ un_mapped_edges$entry1accession[i] <- |
|
| 235 |
+ KEGG_mappings$entryACCESSION[which(KEGG_mappings$entrySYMBOL == |
|
| 236 |
+ un_mapped_edges$entry1symbol[i])][1] |
|
| 237 |
+ un_mapped_edges$entry2accession[i] <- |
|
| 238 |
+ KEGG_mappings$entryACCESSION[which(KEGG_mappings$entrySYMBOL == |
|
| 239 |
+ un_mapped_edges$entry2symbol[i])][1] |
|
| 240 |
+ un_mapped_edges$entry1type[i] <- |
|
| 241 |
+ KEGG_mappings$entryTYPE[which(KEGG_mappings$entrySYMBOL == |
|
| 242 |
+ un_mapped_edges$entry1symbol[i])][1] |
|
| 243 |
+ un_mapped_edges$entry2type[i] <- |
|
| 244 |
+ KEGG_mappings$entryTYPE[which(KEGG_mappings$entrySYMBOL == |
|
| 245 |
+ un_mapped_edges$entry2symbol[i])][1] |
|
| 232 | 246 |
} |
| 233 | 247 |
|
| 234 | 248 |
if (nrow(annotated_edges) > 0 & nrow(un_mapped_edges) > 0) {
|
| 235 | 249 |
all_edges <- gtools::smartbind(annotated_edges, un_mapped_edges) |
| 236 |
- } else if (nrow(annotated_edges) > 0) |
|
| 250 |
+ } else if (nrow(annotated_edges) > 0) |
|
| 237 | 251 |
all_edges <- annotated_edges else {
|
| 238 |
- all_edges <- un_mapped_edges |
|
| 239 |
- all_edges$value <- NA |
|
| 240 |
- all_edges$subtype2 <- NA |
|
| 241 |
- all_edges$value2 <- NA |
|
| 242 |
- all_edges$specific_subtype <- NA |
|
| 243 |
- all_edges$type <- NA |
|
| 244 |
- all_edges$is_direct <- 1 |
|
| 245 |
- all_edges$edgeID <- seq(1:nrow(un_mapped_edges)) |
|
| 246 |
- refcols <- c("edgeID", "entry1accession", "entry2accession", "entry1",
|
|
| 247 |
- "entry2") |
|
| 248 |
- all_edges <- all_edges[, c(refcols, setdiff(names(all_edges), refcols))] |
|
| 249 |
- cat(paste0("All documented edges are of type maplink; only data for
|
|
| 250 |
- de-novo edges can be mapped \n")) |
|
| 251 |
- } |
|
| 252 |
+ all_edges <- un_mapped_edges |
|
| 253 |
+ all_edges$value <- NA |
|
| 254 |
+ all_edges$subtype2 <- NA |
|
| 255 |
+ all_edges$value2 <- NA |
|
| 256 |
+ all_edges$specific_subtype <- NA |
|
| 257 |
+ all_edges$type <- NA |
|
| 258 |
+ all_edges$is_direct <- 1 |
|
| 259 |
+ all_edges$edgeID <- seq(1:nrow(un_mapped_edges)) |
|
| 260 |
+ refcols <- c("edgeID", "entry1accession", "entry2accession", "entry1",
|
|
| 261 |
+ "entry2") |
|
| 262 |
+ all_edges <- all_edges[, c(refcols, setdiff(names(all_edges), refcols))] |
|
| 263 |
+ cat(paste0("All documented edges are of type maplink; only data for
|
|
| 264 |
+ de-novo edges can be mapped \n")) |
|
| 265 |
+ } |
|
| 252 | 266 |
|
| 253 | 267 |
for (i in 1:nrow(all_edges)) {
|
| 254 | 268 |
if (all_edges$entry1[i] == all_edges$entry2[i]) {
|
| ... | ... |
@@ -258,4 +272,4 @@ add_edge_data <- function(expanded_edges, KEGG_mappings, |
| 258 | 272 |
} |
| 259 | 273 |
} |
| 260 | 274 |
return(all_edges) |
| 261 |
-} |
|
| 275 |
+ } |
| ... | ... |
@@ -27,8 +27,9 @@ |
| 27 | 27 |
#' "HA1E", data_type = "100_bing") |
| 28 | 28 |
#' |
| 29 | 29 |
#' p53_edges_HA1E_data_MAPPED <- add_edge_data(p53_edges, p53_KEGG_mappings, |
| 30 |
-#' p53_HA1E_data, c(3, 10,12), |
|
| 31 |
-#' only_mapped = TRUE) |
|
| 30 |
+#' p53_HA1E_data, |
|
| 31 |
+#' data_column_no = c(3, 10,12), |
|
| 32 |
+#' only_mapped = TRUE) |
|
| 32 | 33 |
#' |
| 33 | 34 |
#' p53_edge_mapping_HA1E <- edge_mapping_info(p53_edges_HA1E_data_MAPPED, |
| 34 | 35 |
#' data_added = TRUE) |
| ... | ... |
@@ -4,8 +4,8 @@ |
| 4 | 4 |
\alias{add_edge_data}
|
| 5 | 5 |
\title{Annotate KEGG edge mappings with user data}
|
| 6 | 6 |
\usage{
|
| 7 |
-add_edge_data(expanded_edges, KEGG_mappings, user_data, data_column_no = 3, |
|
| 8 |
- only_mapped = FALSE) |
|
| 7 |
+add_edge_data(expanded_edges, KEGG_mappings, user_data, map_type = "SYMBOL", |
|
| 8 |
+ data_column_no = 3, only_mapped = FALSE) |
|
| 9 | 9 |
} |
| 10 | 10 |
\arguments{
|
| 11 | 11 |
\item{expanded_edges}{The data frame object generated via the function
|
| ... | ... |
@@ -18,6 +18,9 @@ function expand_KEGG_mappings} |
| 18 | 18 |
gene symbols representing an edge and any/all other column[s] contain |
| 19 | 19 |
corresponding edge data.} |
| 20 | 20 |
|
| 21 |
+\item{map_type}{If the genes in your data set are left untranslated
|
|
| 22 |
+set to "NUMBER" (assuming numbers are gene accession numbers)} |
|
| 23 |
+ |
|
| 21 | 24 |
\item{data_column_no}{The column index for desired user data to be added}
|
| 22 | 25 |
|
| 23 | 26 |
\item{only_mapped}{A logical indicator; if set to FALSE will return 'de-novo'
|
| ... | ... |
@@ -43,8 +43,9 @@ p53_HA1E_data <- overlap_info(p53_KGML, p53_KEGG_mappings, |
| 43 | 43 |
"HA1E", data_type = "100_bing") |
| 44 | 44 |
|
| 45 | 45 |
p53_edges_HA1E_data_MAPPED <- add_edge_data(p53_edges, p53_KEGG_mappings, |
| 46 |
- p53_HA1E_data, c(3, 10,12), |
|
| 47 |
- only_mapped = TRUE) |
|
| 46 |
+ p53_HA1E_data, |
|
| 47 |
+ data_column_no = c(3, 10,12), |
|
| 48 |
+ only_mapped = TRUE) |
|
| 48 | 49 |
|
| 49 | 50 |
p53_edge_mapping_HA1E <- edge_mapping_info(p53_edges_HA1E_data_MAPPED, |
| 50 | 51 |
data_added = TRUE) |
