XGR (version 1.1.4)

xRepurpose: Function to obtain repurposing matrix

Description

xRepurpose is supposed to obtain repurposing matrix given a query list of genes. It returns an object of the class 'DR'.

Usage

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",
...)

Arguments

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 xRDataLoader for details

...

additional graphic parameters for xHeatmap

Value

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

See Also

xRDataLoader, xHeatmap

Examples

# 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)
# }