clinicalEnrichment: Performs mutational enrichment analysis for a given clinical...

In maftools: Summarize, Analyze and Visualize MAF Files

Description

Performs pairwise and groupwise fisher exact tests to find differentially enriched genes for every factor within a clinical feature.

Usage

clinicalEnrichment(
  maf,
  clinicalFeature = NULL,
  annotationDat = NULL,
  minMut = 5,
  useCNV = TRUE
)

Arguments

maf	MAF object
clinicalFeature	columns names from 'clinical.data' slot of MAF to be analysed for.
annotationDat	If MAF file was read without clinical data, provide a custom data.frame or a tsv file with a column containing Tumor_Sample_Barcodes along with clinical features. Default NULL.
minMut	Consider only genes with minimum this number of samples mutated. Default 5.
useCNV	whether to include copy number events. Only applicable when MAF is read along with copy number data. Default TRUE if available.

Details

Performs fishers test on 2x2 contingency table for WT/Mutants in group of interest vs rest of the sample. Odds Ratio indicate the odds of observing mutant in the group of interest compared to wild-type

Value

result list containing p-values

See Also

plotEnrichmentResults

Examples

## Not run: 
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)
clinicalEnrichment(laml, 'FAB_classification')

## End(Not run)

Example output

-Reading
-Validating
-Silent variants: 475 
-Summarizing
-Processing clinical data
-Finished in 0.437s elapsed (0.400s cpu) 
Sample size per factor in FAB_classification:

M0 M1 M2 M3 M4 M5 M6 M7 
19 44 44 21 39 19  3  3 
$pairwise_comparision
     Hugo_Symbol Feature_1 Feature_2 n_mutated_Feature1 n_mutated_Feature2
  1:        TP53        M7        M1             3 of 3            2 of 44
  2:        TP53        M7        M3             3 of 3            0 of 21
  3:        TP53        M7        M5             3 of 3            0 of 19
  4:        TP53        M7        M4             3 of 3            2 of 39
  5:        TP53        M7        M2             3 of 3            3 of 44
 ---                                                                      
457:         TTN        M5        M4            1 of 19            2 of 39
458:         TTN        M6        M4             0 of 3            2 of 39
459:         TTN        M7        M4             0 of 3            2 of 39
460:         TTN        M6        M5             0 of 3            1 of 19
461:         TTN        M7        M5             0 of 3            1 of 19
             fdr
  1: 0.005844156
  2: 0.005844156
  3: 0.005844156
  4: 0.005879791
  5: 0.006660500
 ---            
457: 1.000000000
458: 1.000000000
459: 1.000000000
460: 1.000000000
461: 1.000000000

$groupwise_comparision
     Hugo_Symbol Group1 Group2 n_mutated_group1 n_mutated_group2      p_value
  1:        IDH1     M1   Rest         11 of 44         7 of 149 0.0002597371
  2:        TP53     M7   Rest           3 of 3        12 of 190 0.0003857187
  3:      DNMT3A     M5   Rest         10 of 19        38 of 174 0.0057610493
  4:       CEBPA     M2   Rest          7 of 44         6 of 149 0.0117352110
  5:       RUNX1     M0   Rest          5 of 19        11 of 174 0.0117436825
 ---                                                                         
156:       STAG2     M6   Rest           0 of 3         6 of 190 1.0000000000
157:       STAG2     M7   Rest           0 of 3         6 of 190 1.0000000000
158:         TTN     M2   Rest          0 of 44         6 of 149 1.0000000000
159:         TTN     M6   Rest           0 of 3         6 of 190 1.0000000000
160:         TTN     M7   Rest           0 of 3         6 of 190 1.0000000000
     OR_low   OR_high       fdr
  1:      0 0.3926994 0.0308575
  2:      0 0.1315271 0.0308575
  3:      0 0.6406007 0.3072560
  4:      0 0.6874270 0.3757978
  5:      0 0.6466787 0.3757978
 ---                           
156:      0       Inf 1.0000000
157:      0       Inf 1.0000000
158:      0       Inf 1.0000000
159:      0       Inf 1.0000000
160:      0       Inf 1.0000000

$cf_sizes
     cf  N
1:   M4 39
2:   M3 21
3:   M0 19
4:   M1 44
5:   M2 44
6:   M5 19
7:   M6  3
8:   M7  3
9: <NA>  1

$clinicalFeature
[1] "FAB_classification"

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