install.install.packages("~/Documents/ICELLNET/Package/icellnet_0.0.0.9000.tar.gz", repos=NULL, type="source")
install.packages("~/Documents/ICELLNET/Package/icellnet_0.0.0.9000.tar.gz", repos=NULL, type="source")
library(icellnet)
library(curl)
db=read.csv(curl::curl(url="https://raw.githubusercontent.com/soumelis-lab/ICELLNET/master/database.tsv"), sep="\t",header = T, check.names=FALSE)
head(db)
summary(as.factor(db$Family)) # list of the different family of molecules considered in the database
summary(as.factor(db$Subfamily[which(db$Family=="Cytokine")])) # list of the different subfamily of cytokines considered in the database
summary(as.factor(db$Family)) # list of the different family of molecules considered in the database
summary(as.factor(db$Subfamily[which(db$Family=="Cytokine")])) # list of the different subfamily of cytokines considered in the database
#Restrict the database to some family of molecules
my.selection.LR=c("Cytokine", "Chemokine", "Checkpoint")
db2 <- db[grepl(paste(my.selection.LR, collapse="|"),db$Classifications),]
db.name.couple=name.lr.couple(db2, type="Family")
head(db.name.couple)
#Restrict the database to cytokines and consider the subfamilies of cytokines
my.selection.LR=c("Cytokine")
db2
db3 <- db[grepl(paste(my.selection.LR, collapse="|"),db$Classifications),] #if you want to use all the database, do instead : db2=db
head(db3)
db.name.couple=name.lr.couple(db3, type="Subfamily")
db.name.couple
name.lr.couple
db
db[1,2]
db=read.csv(curl::curl(url="https://raw.githubusercontent.com/soumelis-lab/ICELLNET/master/database.tsv"), sep="\t",header = T, check.names=FALSE, stringsAsFactors = FALSE)
head(db)
db=read.csv(curl::curl(url="https://raw.githubusercontent.com/soumelis-lab/ICELLNET/master/database.tsv"), sep="\t",header = T, check.names=FALSE, stringsAsFactors = FALSE)
head(db)
db[1,2]
db=read.table(curl::curl(url="https://raw.githubusercontent.com/soumelis-lab/ICELLNET/master/database.tsv"), sep="\t",header = T, check.names=FALSE, stringsAsFactors = FALSE)
db
db.name.couple
name.lr.couple
db=read.csv(curl::curl(url="https://raw.githubusercontent.com/soumelis-lab/ICELLNET/master/database.tsv"),
sep="\t",header = T, check.names=FALSE, stringsAsFactors = FALSE, colClasses = "character")
db
head(db)
db[1,2]
db=read.csv(curl::curl(url="https://raw.githubusercontent.com/soumelis-lab/ICELLNET/master/database.tsv"),
sep="\t", header = T, check.names=FALSE, stringsAsFactors = FALSE, colClasses = "character", na.strings = ".")
head(db)
db[1,2]
db=read.csv(curl::curl(url="https://raw.githubusercontent.com/soumelis-lab/ICELLNET/master/database.tsv"),
sep="\t", header = T,  colClasses = "character", stringsAsFactors = FALSE, check.names=FALSE)
head(db)
db=read.csv(curl::curl(url="https://raw.githubusercontent.com/soumelis-lab/ICELLNET/master/database.tsv"),
sep="\t", header = T,  colClasses = "character", stringsAsFactors = FALSE, check.names=FALSE, na.strings = NA)
head(db)
db[1,2]
db=read.csv(curl::curl(url="https://raw.githubusercontent.com/soumelis-lab/ICELLNET/master/database.tsv"),
sep="\t", header = T,  colClasses = "character", stringsAsFactors = FALSE, check.names=FALSE, na.strings = "")
head(db)
db[1,2]
db=read.csv(curl::curl(url="https://raw.githubusercontent.com/soumelis-lab/ICELLNET/master/database.tsv"), sep="\t",header = T, check.names=FALSE, stringsAsFactors = FALSE, na.strings = "")
head(db)
summary(as.factor(db$Family)) # list of the different family of molecules considered in the database
summary(as.factor(db$Subfamily[which(db$Family=="Cytokine")])) # list of the different subfamily of cytokines considered in the database
#Restrict the database to some family of molecules
my.selection.LR=c("Cytokine", "Chemokine", "Checkpoint")
db.name.couple=name.lr.couple(db2, type="Family")
db2
db.name.couple=name.lr.couple(db2, type="Family")
db.name.couple=name.lr.couple(db2, type="Family")
head(db.name.couple)
db
db=read.csv(curl::curl(url="https://raw.githubusercontent.com/soumelis-lab/ICELLNET/master/database.tsv"), sep="\t",header = T, check.names=FALSE, stringsAsFactors = FALSE, na.strings = "")
head(db)
summary(as.factor(db$Family)) # list of the different family of molecules considered in the database
summary(as.factor(db$Subfamily[which(db$Family=="Cytokine")])) # list of the different subfamily of cytokines considered in the database
db
db.name.couple=name.lr.couple(db2, type="Family")
head(db.name.couple)
name.lr.couple
db2
db=read.csv(curl::curl(url="https://raw.githubusercontent.com/soumelis-lab/ICELLNET/master/database.tsv"), sep="\t",header = T, check.names=FALSE, stringsAsFactors = FALSE, na.strings = "")
summary(as.factor(db$Family)) # list of the different family of molecules considered in the database
#Restrict the database to some family of molecules
my.selection.LR=c("Cytokine", "Chemokine", "Checkpoint")
db.name.couple=name.lr.couple(db2, type="Family")
head(db.name.couple)
name.lr.couple
db$Subfamily
my.selection.LR
db$Classifications
head(db)
db2 <- db[grepl(paste(my.selection.LR, collapse="|"),db$Classifications),]
name.lr.couple
