dnet 1.1.2

Transcriptome dataset for Chronic Lymphocytic Leukemia patients from Chuang et al. (2012)

Description

This dataset involves 130 patients with chronic lymphocytic leukemia (CLL). When enrolled in the study, these CLL patients had not received prior therapy for CLL. Additional covariate about the time to treatment (i.e. prognosis) is available. The dataset has been normalised and log2-transformed, and provided as an 'ExpressionSet' object.

Usage

CLL <- dRDataLoader(RData = "CLL")

Value

an object of class "ExpressionSet". It has slots for "assayData", "phenoData", and "featureData":

  • assayData: a matrix of 54675 features X 130 samples
  • phenoData: variables describing sample phenotypes (i.e. columns in assayData), including information about samples: "Name" for sample names, "Time" for sampling time to first treatment (years) and "Treatment" for treatment event (1:yes, 0:no)
  • featureData: variables describing features (i.e. rows in assayData), including information about features/genes: "EntrezID" for gene EntrezID, "Symbol" for gene symbol and "Desc" for gene description

References

Chuang et al. (2012). Subnetwork-based analysis of chronic lymphocytic leukemia identifies pathways that associate with disease progression. Blood, 120(13):2639-49.

Examples

CLL <- dRDataLoader(RData='CLL')


'CLL' (from https://github.com/hfang-bristol/RDataCentre/blob/master/dnet/1.0.7/CLL.RData?raw=true) has been loaded into the working environment (at 2018-01-19 12:34:29)

CLL



ExpressionSet (storageMode: lockedEnvironment)
assayData: 54675 features, 130 samples 
  element names: exprs 
protocolData: none
phenoData
  sampleNames: GSM977137 GSM977138 ... GSM977266 (130 total)
  varLabels: Name Time Treatment
  varMetadata: labelDescription
featureData
  featureNames: 1007_s_at 1053_at ... AFFX-TrpnX-M_at (54675 total)
  fvarLabels: EntrezID Symbol Desc
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
Annotation:  



library(Biobase)
# extract information about the first 5 samples
pData(CLL)[1:5,]



          Name     Time Treatment
GSM977137 CLL1 2.487671         1
GSM977138 CLL2 3.084932         1
GSM977139 CLL3 2.882192         1
GSM977140 CLL4 0.109589         1
GSM977141 CLL5 3.249315         0



# extract information about the first 5 features
fData(CLL)[1:5,]



          EntrezID Symbol                                        Desc
1007_s_at                                                  NA
1053_at       5982   RFC2 replication factor C (activator 1) 2, 40kDa
117_at        3310  HSPA6        heat shock 70kDa protein 6 (HSP70B')
121_at        7849   PAX8                                paired box 8
1255_g_at     2978 GUCA1A     guanylate cyclase activator 1A (retina)