rnaCrosslinkQC: rnaCrosslinkQC

In JLP-BioInf/comradesOO: Analysis of RNA Crosslinking Data

rnaCrosslinkQC

Description

get a plot fo the read lengths and transcripts in the dataset The fucntion will make 1 pdf and 2 text file in the directory provided

Usage

rnaCrosslinkQC(sampleTable, directory, topTranscripts = TRUE)

Arguments

sampleTable	string - The address of the sample table, the sample table must have 4 columns, fileName (the full path and file name of the input Input file for each sample ), group ("s" - sample or "c" - control), sample (1,2,3, etc), sampleName (must be unique).
directory	A directory address to write the files
topTranscripts	If FALSE a table of top trandscirpts will not be written to file

Value

ggplot and txt file

Examples

  c4 = c(rep("transcript1",100),rep("transcript2",100) )
 c10 = c(rep("transcript1",200) )
 c1 = 1:200
 c2 = rep(paste(rep("A", 40), collapse = ""),200)
 c3 = rep(".",200)
 c9 = rep(".",200)
 c15 = rep(".",200)
 c5 = rep(1,200)
 c11 = rep(21,200)
 c6 = rep(20,200)
 c12= rep(40,200)
 # short distance 50
 c7 = sample(1:5, 50, replace = TRUE)
 c8 = sample(20:25, 50, replace = TRUE)
 c13 = sample(20:25, 50, replace = TRUE)
 c14 = sample(40:45, 50, replace = TRUE)
 # long distance 50
 c7 = c(c7,sample(1:5, 50, replace = TRUE))
 c8 = c(c8,sample(20:25, 50, replace = TRUE))
 c13 = c(c13,sample(60:70, 50, replace = TRUE))
 c14 = c(c14,sample(80:83, 50, replace = TRUE))
 # inter RNA 100
 c7 = c(c7,sample(1:5, 100, replace = TRUE))
 c8 = c(c8,sample(20:25, 100, replace = TRUE))
 c13 = c(c13,sample(1:5, 100, replace = TRUE))
 c14 = c(c14,sample(20:25, 100, replace = TRUE))
 
 exampleInput = data.frame(V1 = c1,
                           V2 = c2,
                           V3 = c3,
                           V4 = c4,
                           V5 = as.numeric(c5),
                           V6 = as.numeric(c6),
                           V7 = as.numeric(c7),
                           V8 = as.numeric(c8),
                           V9 = c9,
                           V10 = c10,
                           V11 = as.numeric(c11),
                           V12 = as.numeric(c12),
                           V13 = as.numeric(c13),
                           V14 = as.numeric(c14),
                           V15 = c15)
 
 
 file = tempfile()
 write.table(exampleInput,
             file = file, 
             quote = FALSE,
             row.names = FALSE, 
             sep = "\t", col.names = FALSE)
 
 
 
 
 c4 = c(rep("transcript1",55),rep("transcript2",90) )
 c10 = c(rep("transcript1",145) )
 c1 = 1:145
 c2 = rep(paste(rep("A", 40), collapse = ""),145)
 c3 = rep(".",145)
 c9 = rep(".",145)
 c15 = rep(".",145)
 c5 = rep(1,145)
 c11 = rep(21,145)
 c6 = rep(20,145)
 c12= rep(40,145)
 # short distance 55
 c7 = sample(1:5, 55, replace = TRUE)
 c8 = sample(20:25, 55, replace = TRUE)
 c13 = sample(20:25, 55, replace = TRUE)
 c14 = sample(40:45, 55, replace = TRUE)
 
 # inter RNA 100
 c7 = c(c7,sample(1:40, 90, replace = TRUE))
 c8 = c(c8,sample(20:75, 90, replace = TRUE))
 c13 = c(c13,sample(1:40, 90, replace = TRUE))
 c14 = c(c14,sample(20:75, 90, replace = TRUE))
 
 exampleInput = data.frame(V1 = c1,
                           V2 = c2,
                           V3 = c3,
                           V4 = c4,
                           V5 = as.numeric(c5),
                           V6 = as.numeric(c6),
                           V7 = as.numeric(c7),
                           V8 = as.numeric(c8),
                           V9 = c9,
                           V10 = c10,
                           V11 = as.numeric(c11),
                           V12 = as.numeric(c12),
                           V13 = as.numeric(c13),
                           V14 = as.numeric(c14),
                           V15 = c15)
 
 
file2 = tempfile()
 write.table(exampleInput,
             file = file2, 
             quote = FALSE, 
             row.names = FALSE, 
             sep = "\t",
             col.names = FALSE)

 
 # Set up the sample table. ----
 sampleTabler1 = c(file, "s", "1", "s1")
 sampleTabler2 = c(file2, "c", "1", "c1")
 # make the sample table 
 sampleTable2 = rbind.data.frame(sampleTabler1, sampleTabler2)
 # add the column names 
 colnames(sampleTable2) = c("file", "group", "sample", "sampleName")

rnaCrosslinkQC(sampleTable2,tempdir())

JLP-BioInf/comradesOO documentation built on April 28, 2024, 4:22 a.m.