rnaCrosslinkDataSet-class {rnaCrosslinkOO}

rnaCrosslinkDataSet

Description

rnaCrosslinkDataSet 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 Input files are also filtered for the RNA of interest. Check the package vignette for more information.

Usage

rnaCrosslinkDataSet(
  rnas,
  rnaSize = 0,
  sampleTable,
  subset = "all",
  sample = "all"
)

Arguments

rnas

vector - The names of the RNA interest, these must be displayed the same way as in the input Input 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 Input file for each sample ), group ("s" - sample or "c" - control), sample (1,2,3, etc), sampleName (must be unique).

subset

a vector of 4 values to subset based on structural read size. c(l-min,l-max,r-min,r-max)

sample

The number of reads to sample for each sample.

Value

A rnaCrosslinkDataSet 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 rnaCrosslinkDataSet 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 rnaCrosslinkDataSet 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 rnaCrosslinkDataSet objects, matrixList(cds)[[rna]][[type]][[sample]]. Contains a set of contact matrices, each cell contains the number of duplexes identified for position x,y.

InputFiles

List - Follows the pattern for list slots of rnaCrosslinkDataSet objects, InputFiles(cds)[[rna]][[type]][[sample]]. Contains a set of tables, these are the original Input 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
cds = makeExamplernaCrosslinkDataSet()

cds