cpData: Method that returns the 'dataFull' slot in a 'CancerPanel'...
In PrecisionTrialDrawer: A Tool to Analyze and Design NGS Based Custom Gene Panels

Description Usage Arguments Details Value Author(s) References See Also Examples

This method returns a list with an element for each alteration type contained in the class CancerPanel slot dataFull

1	cpData(object)

object

a CancerPanel object

The length of the output list is always defined by 4 elements even if no data, for a certain alteration type, were requested.In case no data were requested or if there are no data for a certain tumor type, the slot is filled with NULL values. Every element is a list of 2 elements:

data A data.frame in a format specific for the alteration type.
Samples The second element is a list of vectors containing the names of the samples for each tumor type.

A list of 4 elements, one for each alteration type:

`mutations`	A list of 2 elements containing the mutation alterations for each gene requested in the panel.
`copynumber`	A list of 2 elements containing the copynumber alterations for each gene requested in the panel.
`expression`	A list of 2 elements containing the expression alterations for each gene requested in the panel.
`fusions`	A list of 2 elements containing the fusions alterations for each gene requested in the panel.

Giorgio Melloni , Alessandro Guida

data origin for mutations, copynumber and expression data data origin for fusion data

cpDataSubset

# Load example CancerPanel object
data(cpObj2)
# Show slot dataSubset
str( cpData(cpObj2) )

Creating a generic function for ‘toJSON’ from package ‘jsonlite’ in package ‘googleVis’
List of 4
 $ fusions   :List of 2
  ..$ data   : NULL
  ..$ Samples: NULL
 $ mutations :List of 2
  ..$ data   :'data.frame':	59 obs. of  9 variables:
  .. ..$ entrez_gene_id    : int [1:59] 7157 7157 7157 7157 7157 7157 7157 7157 7157 7157 ...
  .. ..$ gene_symbol       : chr [1:59] "TP53" "TP53" "TP53" "TP53" ...
  .. ..$ case_id           : chr [1:59] "TCGA-AB-2820" "TCGA-AB-2860" "TCGA-AB-2943" "TCGA-AB-2935" ...
  .. ..$ mutation_type     : chr [1:59] "Frame_Shift_Ins" "Frame_Shift_Ins" "Missense_Mutation" "Missense_Mutation" ...
  .. ..$ amino_acid_change : chr [1:59] "P223Rfs*4" "M40Lfs*7" "R273C" "R248Q" ...
  .. ..$ genetic_profile_id: chr [1:59] "laml_tcga_pub" "laml_tcga_pub" "laml_tcga_pub" "laml_tcga_pub" ...
  .. ..$ tumor_type        : chr [1:59] "laml" "laml" "laml" "laml" ...
  .. ..$ amino_position    : num [1:59] 223 40 273 248 193 176 317 126 179 280 ...
  .. ..$ genomic_position  : chr [1:59] "17:7578181:NA,GCGGCTC" "17:7579569:NA,CCATCCAG" "17:7577121:G,A" "17:7577538:C,T" ...
  ..$ Samples:List of 1
  .. ..$ laml: chr [1:200] "TCGA-AB-2803" "TCGA-AB-2804" "TCGA-AB-2806" "TCGA-AB-2815" ...
 $ copynumber:List of 2
  ..$ data   : NULL
  ..$ Samples: NULL
 $ expression:List of 2
  ..$ data   : NULL
  ..$ Samples: NULL