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# Secretome Lysat Peptide Descriptor
#
# functions to get infos from the gff-data.frame
# getTopofeatures extract a vector that shows the belonging to the topological domains for
# every aminoacid of the protein
# Input: data.frame GffHuman, numerical vector proteinlength, character vector accession
# Output: logical vector result, character vector topo, data.frame topodf
getTopofeatures <- function(gff,protl, acc)
{
topo <- rep("no",protl)
topodf <- data.frame(feature=character(), start= numeric(), end=numeric())
mygff <- gff[gff$seqname == acc, ]
result <- FALSE
signal <- mygff[mygff$feature == "Signal peptide", c("feature", "start", "end")]
if(nrow(signal) > 0)
{
for (i in seq_along(signal$start))
{
topo[signal$start[i]:signal$end[i]] <- "SP"
}
signal$feature <- "SP"
topodf <- rbind(topodf,signal)
result <- TRUE
}
transm <- mygff[mygff$feature == "Transmembrane", c("feature","start", "end")]
if(nrow(transm) > 0)
{
for (i in seq_along(transm$start))
{
topo[transm$start[i]:transm$end[i]] <- "TM"
}
transm$feature <- "TM"
topodf <- rbind(topodf,transm)
result <- TRUE
}
extra <- mygff[mygff$feature == "Topological domain" & mygff$Note == "Extracellular", c("feature","start", "end")]
if(nrow(extra) >0)
{
for (i in seq_along(extra$start))
{
topo[extra$start[i]:extra$end[i]] <- "EC"
}
extra$feature <- "EC"
topodf <- rbind(topodf,extra)
result <- TRUE
}
cyto <- mygff[mygff$feature == "Topological domain" & mygff$Note == "Cytoplasmic", c("feature","start", "end")]
if(nrow(cyto) >0)
{
for (i in seq_along(cyto$start))
{
topo[cyto$start[i]:cyto$end[i]] <- "CP"
}
cyto$feature <- "CP"
topodf <- rbind(topodf,cyto)
result <- TRUE
}
return <- list(result,topo,topodf)
}
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