xRepurpose | R Documentation |
xRepurpose
is supposed to obtain repurposing matrix given a
query list of genes. It returns an object of the class 'DR'.
xRepurpose(data, phase.min = 3, target.max = 5, plot = TRUE, verbose = T, DTT = c("ChEMBL_v24", "ChEMBL_v23"), restricted = NULL, excluded = NULL, RData.location = "http://galahad.well.ox.ac.uk/bigdata", ...)
data |
an input vector containing gene symbols |
phase.min |
the minumum phase of drugs allowed. By default it is 3 defining target genes of drugs reaching development phase 3 and above |
target.max |
the maximum number of targets per drug allowed. By default it is 5. It is used to define non-promoscuous drug target genes |
plot |
logical to indicate whether heatmap plot is drawn |
verbose |
logical to indicate whether the messages will be displayed in the screen. By default, it sets to true for display |
DTT |
the drug therapeutic targets. It can be "ChEMBL_v24" for the version 24 (by default), and the version 23. Note: you can also load your customised object directly with columns ('target_number','efo_term','phase','pref_name_drug','Symbol') |
restricted |
the disease areas restricted to. By default it is NULL |
excluded |
the disease areas that are excluded. By default it is NULL |
RData.location |
the characters to tell the location of built-in
RData files. See |
... |
additional graphic parameters for xHeatmap |
an object of class "DR", a list with following components:
df
: a data frame of n x 5, where the 5 columns are
"Target", "Disease", "Phase", "Drug", "Drug_index"
index
: a data frame of n x 2, where the 2 columns are
"Drug_index", "Drug"
gp
: NULL if the plot is not drawn; otherwise, a 'ggplot'
object
none
xRDataLoader
, xHeatmap
## Not run: # Load the library library(XGR) RData.location <- "http://galahad.well.ox.ac.uk/bigdata/" # a) provide the input Genes of interest (eg 1000 randomly chosen human genes) ## load human genes org.Hs.eg <- xRDataLoader(RData='org.Hs.eg', RData.location=RData.location) set.seed(825) data <- as.character(sample(org.Hs.eg$gene_info$Symbol, 1000)) # b) obtain repurposing matrix DR <- xRepurpose(data, RData.location=RData.location, reorder="none", colormap="ggplot2.top", zlim=c(1,4), na.color='transparent', label.size=1.5, label.color="white") DR$gp write.table(DR$df, file="xRepurpose.txt", sep="\t", row.names=F, quote=F) write.table(DR$index, file="xRepurpose_index.txt", sep="\t", row.names=F, quote=F) ## End(Not run)