Nothing
matchFeatures <-
function (CN = NULL, Exp = NULL, CN.by.feat = c("gene", "probe"),
Exp.by.feat = c("gene", "probe"), ref = "hg19")
{
if (length(CN.by.feat) == 2) {
CN.by.feat <- "probe"
}
if (length(Exp.by.feat) == 2) {
Exp.by.feat <- "gene"
}
IntClustMemb <- NULL
data(Map.CN, envir = environment())
data(Map.Exp, envir = environment())
data(train.CN, envir = environment())
data(train.Exp, envir = environment())
data(IntClustMemb, envir = environment())
data(Map.All, envir = environment())
if (!is.null(CN) & is.null(Exp)) {
if (CN.by.feat == "probe") {
Probes <- Map.All$Probe_ID
Synonyms <- NULL
train.CN <- as.matrix(train.CN)
}
else {
Map.All <- Map.All[which(Map.All$Gene.Chosen == "YES"),
]
Probes <- as.character(Map.All$Gene_symbol)
Synonyms <- as.character(Map.All$Synonyms_0)
tmp <- rep(Probes, sapply(strsplit(Synonyms, ";"),
length))
Synonyms <- do.call("c", strsplit(Synonyms, ";"))
Synonyms <- gsub(" ", "", Synonyms)
names(Synonyms) <- tmp
Synonyms <- Synonyms[which(!is.na(Synonyms))]
train.CN <- as.matrix(train.CN[Map.All$Probe_ID,
])
rownames(train.CN) <- Map.All$Gene_symbol
}
CN <- getCNfeatures(CN, Probes, Map.All, CN.by.feat,
ref, Synonyms)
all.na <- which(apply(CN, 1, function(x) mean(is.na(x))) <
1)
CN <- CN[all.na, , drop=F]
train.CN <- train.CN[all.na, ]
Map.CN <- Map.All[all.na, ]
Map.Exp <- NULL
train.Exp <- NULL
}
if (!is.null(CN) & !is.null(Exp)) {
if (Exp.by.feat == "probe") {
Probes <- Map.Exp$Probe_ID
Synonyms <- as.character(Map.Exp$Synonyms_0)
tmp <- rep(Probes, sapply(strsplit(Synonyms, ";"),
length))
Synonyms <- do.call("c", strsplit(Synonyms, ";"))
Synonyms <- gsub(" ", "", Synonyms)
names(Synonyms) <- tmp
Synonyms <- Synonyms[which(!is.na(Synonyms))]
train.Exp <- train.Exp[Map.Exp$Probe_ID, ]
}
else {
Map.Exp <- Map.Exp[which(Map.Exp$Gene.Chosen == "YES"),
]
Probes <- as.character(Map.Exp$Gene_symbol)
Synonyms <- as.character(Map.Exp$Synonyms_0)
tmp <- rep(Probes, sapply(strsplit(Synonyms, ";"),
length))
Synonyms <- do.call("c", strsplit(Synonyms, ";"))
Synonyms <- gsub(" ", "", Synonyms)
names(Synonyms) <- tmp
Synonyms <- Synonyms[which(!is.na(Synonyms))]
train.Exp <- train.Exp[Map.Exp$Probe_ID, ]
rownames(train.Exp) <- Map.Exp$Gene_symbol
}
if (CN.by.feat == "probe") {
Probes.CN <- Map.CN$Probe_ID
Synonyms.CN <- NULL
train.CN <- as.matrix(train.CN[Map.CN$Probe_ID, ])
}
else {
tmp.map <- Map.All[, c("Probe_ID", "Synonyms_0")]
Map.CN <- merge(Map.CN, tmp.map, sort = FALSE)
rownames(Map.CN) <- Map.CN$Probe_ID
Probes.CN <- as.character(Map.CN$Gene_symbol)
Synonyms.CN <- as.character(Map.CN$Synonyms_0)
tmp <- rep(Probes.CN, sapply(strsplit(Synonyms.CN,
";"), length))
Synonyms.CN <- do.call("c", strsplit(Synonyms.CN,
";"))
Synonyms.CN <- gsub(" ", "", Synonyms.CN)
names(Synonyms.CN) <- tmp
Synonyms.CN <- Synonyms.CN[which(!is.na(Synonyms.CN))]
train.CN <- as.matrix(train.CN[rownames(Map.CN),
])
rownames(train.CN) <- Map.CN$Gene_symbol
}
CN <- getCNfeatures(CN, Probes.CN, Map.CN, CN.by.feat,
ref, Synonyms.CN)
Exp <- getExpfeatures(Exp, Probes, Synonyms, Exp.by.feat)
common.cols <- intersect(colnames(Exp), colnames(CN))
Exp <- Exp[, which(colnames(Exp) %in% common.cols)]
CN <- CN[, which(colnames(CN) %in% common.cols)]
CN <- CN[, match(colnames(Exp), colnames(CN))]
all.na <- which(apply(Exp, 1, function(x) mean(is.na(x))) <
1)
Exp <- Exp[all.na, ]
train.Exp <- train.Exp[all.na, ]
Map.Exp <- Map.Exp[all.na, ]
all.na <- which(apply(CN, 1, function(x) mean(is.na(x))) <
1)
CN <- CN[all.na, , drop=F]
train.CN <- train.CN[all.na, ]
Map.CN <- Map.CN[all.na, ]
train.Exp <- as.matrix(train.Exp)
}
if (!is.null(Exp) & is.null(CN)) {
if (Exp.by.feat == "probe") {
Probes <- Map.All$Probe_ID
Synonyms <- as.character(Map.All$Synonyms_0)
tmp <- rep(Probes, sapply(strsplit(Synonyms, ";"),
length))
Synonyms <- do.call("c", strsplit(Synonyms, ";"))
Synonyms <- gsub(" ", "", Synonyms)
names(Synonyms) <- tmp
Synonyms <- Synonyms[which(!is.na(Synonyms))]
}
else {
Map.All <- Map.All[which(Map.All$Gene.Chosen == "YES"),
]
Probes <- as.character(Map.All$Gene_symbol)
Synonyms <- as.character(Map.All$Synonyms_0)
tmp <- rep(Probes, sapply(strsplit(Synonyms, ";"),
length))
Synonyms <- do.call("c", strsplit(Synonyms, ";"))
Synonyms <- gsub(" ", "", Synonyms)
names(Synonyms) <- tmp
Synonyms <- Synonyms[which(!is.na(Synonyms))]
train.Exp <- train.Exp[Map.All$Probe_ID, ]
rownames(train.Exp) <- Map.All$Gene_symbol
}
Exp <- getExpfeatures(Exp, Probes, Synonyms, Exp.by.feat)
all.na <- which(apply(Exp, 1, function(x) mean(is.na(x))) <
1)
Exp <- Exp[all.na, ]
train.Exp <- train.Exp[all.na, ]
train.CN <- NULL
train.Exp <- as.matrix(train.Exp)
Map.CN <- NULL
Map.Exp <- Map.All[all.na, ]
}
res <- list(CN = CN, Exp = Exp, train.CN = train.CN, train.Exp = train.Exp,
train.iC10 = IntClustMemb, map.cn = Map.CN, map.exp = Map.Exp)
attr(res, "CN.by.feat") <- CN.by.feat
attr(res, "Exp.by.feat") <- Exp.by.feat
attr(res, "ref") <- ref
res
}
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.