View source: R/rnaCrosslinkDataSet.R
rnaCrosslinkDataSet-class | R Documentation |
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.
rnaCrosslinkDataSet(
rnas,
rnaSize = 0,
sampleTable,
subset = "all",
sample = "all"
)
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 |
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. |
A rnaCrosslinkDataSet object.
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
# make example input
cds = makeExamplernaCrosslinkDataSet()
cds
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