comparison report_clonality/RScript.r @ 67:69a6bba9ada9 draft

Uploaded

66:7696dd687f39

  install.packages("data.table", repos="http://cran.xl-mirror.nl/") 
}
library(data.table)

if (!("reshape2" %in% rownames(installed.packages()))) {
  install.packages("reshape2", repos="http://cran.xl-mirror.nl/") 
}
library(reshape2)

if (!("lymphclon" %in% rownames(installed.packages()))) {
  install.packages("lymphclon", repos="http://cran.xl-mirror.nl/") 
}
library(lymphclon)

# ---------------------- parameters ----------------------

count = rbind(sample.count, rep.count)



write.table(x=count, file="productive_counting.txt", sep=",",quote=F,row.names=F,col.names=F)

# ---------------------- Frequency calculation for V, D and J ----------------------

print("Report Clonality - frequency calculation V, D and J")

67:69a6bba9ada9

  install.packages("data.table", repos="http://cran.xl-mirror.nl/") 
}
library(data.table)

if (!("reshape2" %in% rownames(installed.packages()))) {
  install.packages("reshape2", repos="http://cran.xl-mirror.nl/")
}
library(reshape2)

if (!("lymphclon" %in% rownames(installed.packages()))) {
  install.packages("lymphclon", repos="http://cran.xl-mirror.nl/")
}
library(lymphclon)

# ---------------------- parameters ----------------------

count = rbind(sample.count, rep.count)



write.table(x=count, file="productive_counting.txt", sep=",",quote=F,row.names=F,col.names=F)

# ---------------------- V+J+CDR3 sequence count ----------------------

VJCDR3.count = data.frame(table(clonalityFrame$Top.V.Gene, clonalityFrame$Top.J.Gene, clonalityFrame$CDR3.Seq.DNA))
names(VJCDR3.count) = c("Top.V.Gene", "Top.J.Gene", "CDR3.Seq.DNA", "Count")

VJCDR3.count = VJCDR3.count[VJCDR3.count$Count > 0,]
VJCDR3.count = VJCDR3.count[order(-VJCDR3.count$Count),]

write.table(x=VJCDR3.count, file="VJCDR3_count.txt", sep="\t",quote=F,row.names=F,col.names=T)

# ---------------------- Frequency calculation for V, D and J ----------------------

print("Report Clonality - frequency calculation V, D and J")