survGroup: Predict genesets associated with survival

In maftools: Summarize, Analyze and Visualize MAF Files

Description

Predict genesets associated with survival

Usage

survGroup(
  maf,
  top = 20,
  genes = NULL,
  geneSetSize = 2,
  minSamples = 5,
  clinicalData = NULL,
  time = "Time",
  Status = "Status",
  verbose = TRUE
)

Arguments

maf	an MAF object generated by read.maf
top	If genes is NULL by default used top 20 genes
genes	Manual set of genes
geneSetSize	Default 2
minSamples	minimum number of samples to be mutated to be considered for analysis. Default 5
clinicalData	dataframe containing events and time to events. Default looks for clinical data in annotation slot of MAF.
time	column name contining time in clinicalData
Status	column name containing status of patients in clinicalData. must be logical or numeric. e.g, TRUE or FALSE, 1 or 0.
verbose	Default TRUE

Examples

laml.maf <- system.file("extdata", "tcga_laml.maf.gz", package = "maftools")
laml.clin <- system.file("extdata", "tcga_laml_annot.tsv", package = "maftools")
laml <- read.maf(maf = laml.maf,  clinicalData = laml.clin)
survGroup(maf = laml, top = 20, geneSetSize = 1, time = "days_to_last_followup", Status = "Overall_Survival_Status")

Example output

-Reading
-Validating
-Silent variants: 475 
-Summarizing
-Processing clinical data
-Finished in 0.629s elapsed (0.428s cpu) 
------------------
genes: 20
geneset size: 1
20 combinations
Looking for clinical data in annoatation slot of MAF..
Removed 11 samples with NA's
Geneset:  FLT3 [N= 52 ]
Geneset:  DNMT3A [N= 48 ]
Geneset:  NPM1 [N= 33 ]
Geneset:  IDH2 [N= 20 ]
Geneset:  IDH1 [N= 18 ]
Geneset:  TET2 [N= 17 ]
Geneset:  RUNX1 [N= 16 ]
Geneset:  TP53 [N= 15 ]
Geneset:  NRAS [N= 15 ]
Geneset:  CEBPA [N= 13 ]
Geneset:  WT1 [N= 12 ]
Geneset:  PTPN11 [N= 9 ]
Geneset:  KIT [N= 8 ]
Geneset:  KRAS [N= 8 ]
Geneset:  U2AF1 [N= 8 ]
Geneset:  SMC3 [N= 7 ]
Geneset:  PHF6 [N= 6 ]
Geneset:  SMC1A [N= 6 ]
Geneset:  STAG2 [N= 6 ]
Geneset:  TTN [N= 6 ]
    Gene_combination  P_value    hr  WT Mutant
 1:             TP53 6.78e-06 3.540 168     14
 2:           DNMT3A 6.88e-04 1.980 137     45
 3:            RUNX1 3.28e-02 1.860 167     15
 4:             FLT3 1.13e-01 1.380 133     49
 5:             SMC3 1.24e-01 1.870 175      7
 6:             KRAS 3.20e-01 1.470 174      8
 7:            SMC1A 3.21e-01 1.510 176      6
 8:            STAG2 3.31e-01 0.506 176      6
 9:              KIT 4.78e-01 0.695 174      8
10:            U2AF1 4.88e-01 1.310 174      8
11:              WT1 5.55e-01 0.793 171     11
12:           PTPN11 5.74e-01 1.240 173      9
13:             NRAS 6.30e-01 0.840 168     14
14:              TTN 6.75e-01 1.230 177      5
15:             IDH2 7.20e-01 1.110 164     18
16:             NPM1 7.42e-01 1.080 149     33
17:             IDH1 8.13e-01 0.928 165     17
18:            CEBPA 8.56e-01 0.936 170     12
19:             TET2 9.60e-01 1.010 165     17
20:             PHF6 9.98e-01 0.999 176      6

maftools documentation built on Feb. 6, 2021, 2 a.m.