Supported Data Types

Data Type (Parameter)	Description	Output Object ( FirehoseData)
Clinic	Provides clinical information for each sample. Clinical information may include stage, survival time, sex, age and more.	fd@Clinical (data frame)
RNAseq_Gene or/and  RNAseq2_Gene_Norm	Gene level expression data from RNA-seq platforms. This parameter provides raw counts and normalized values. Firehose provides 2 different algorithms for RNAseq data processing. (Data types can be specified by using RNAseqNorm and RNAseq2Norm parameters)	fd@ RNASeqGene, fd@ RNASeq2GeneNorm (data matrix)
miRNASeq_Gene	miRNA expression levels from next generation sequencing platforms	fd@ miRNASeqGene (data matrix)
CNA_SNP	Segmented copy number alterations (in somatic cells)	fd@ CNASNP (data frame)
CNV_SNP	Segmented copy number variations (in germline cells)	fd@ CNVSNP (data frame)
CNA_Seq	Copy number alterations provided by next generation sequencing platforms	fd@ CNAseq (data frame)
CNA_CGH	Copy number alterations provided by CGH array platforms	fd@ CNACGH (a list of FirehoseCGHArray objects )
Methylation	Methylation data provided by array platforms	fd@ Methylation (a list of FirehoseMethylationArray object)
Mutation	Gene level mutation information matrix	fd@ Mutations (data frame)
mRNA_Array	Gene level expression data provided by array platforms	fd@ mRNAArray(a list of FirehosemRNAArray objects )
miRNA_Array	miRNA expression data provided by array platforms	fd@ miRNAArray (a list of  FirehosemRNAArray objects)
RPPA	Reverse phase protein array (RPPA) expression	fd@ RPPAArray(a list of  FirehosemRNAArray objects)