comradesDataSet: comradesDataSet

In comradesOO: Analysis of COMRADES (Cross-Linking Matched RNA and Deep Sequencing) Data

comradesDataSet

Description

comradesDataSet objects are used to store the input meta-data, data and create a framework for the storage of results. Whilst creating the object, the original hyb files are also filtered for the RNA of interest. Check the package vignette for more information.

Usage

comradesDataSet(rnas, rnaSize = 0, sampleTable)

Arguments

rnas	vector - The names of the RNA interest, these must be displayed the same way as in the input Hyb Files.
rnaSize	named list - The sizes (nt) of the RNAs of interest, the list elements must have same names as the rnas vector and each each contain one numeric value.
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 hyb file for each sample ), group ("s" - sample or "c" - control), sample (1,2,3, etc), sampleName (must be unique).

Value

A comradesDataSet object.

Slots

clusterTableFolded

table - a table similar to the clusterTableList it contains coordinates of the clusters along with vienna format fold and RNA sequences for each cluster

clusterTableList

List - Follows the pattern for list slots of comradesDataSet objects, matrixList(cds)[[rna]][[type]][[sample]]. contains a table with coordinates and information about the clusters identified

clusterGrangesList

List - Follows the pattern for list slots of comradesDataSet objects, matrixList(cds)[[rna]][[type]][[sample]]. contains GRanges objects of the original duplexes with their cluster membership

sampleTable

table - Column names; fileName, group (s or c), sample (1,2,3, etc), sampleName (must be unique)

rnas

string - a single RNA to analyse - must be present in rnas(cdsObject)

rnaSize

if set to 0 this will be calculated

matrixList

List - Follows the pattern for list slots of comradesDataSet objects, matrixList(cds)[[rna]][[type]][[sample]]. Contains a set of contact matrices, each cell contains the number of duplexes identified for position x,y.

hybFiles

List - Follows the pattern for list slots of comradesDataSet objects, hybFiles(cds)[[rna]][[type]][[sample]]. Contains a set of tables, these are the original Hyb files that were read in.

interactionTable

Table of interactions discovered in step1 of the folding

viennaStructures

List of vienna format structures from final prediction

dgs

List of free energies

Examples

# make example input
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)


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

# Choose RNA and set up the object ----
rna = c("transcript1")


# load the object
cds = comradesDataSet(rnas = rna,
                     rnaSize = 0,
                     sampleTable = sampleTable2)

cds

comradesOO documentation built on Nov. 10, 2023, 5:08 p.m.