getCytobandSummary: extract cytoband summary from GISTIC object

In maftools: Summarize, Analyze and Visualize MAF Files

Description

extract cytoband summary from GISTIC object

Usage

getCytobandSummary(x)

## S4 method for signature 'GISTIC'
getCytobandSummary(x)

Arguments

x	An object of class GISTIC

Value

summarizied gistic results by altered cytobands.

Examples

all.lesions <- system.file("extdata", "all_lesions.conf_99.txt", package = "maftools")
amp.genes <- system.file("extdata", "amp_genes.conf_99.txt", package = "maftools")
del.genes <- system.file("extdata", "del_genes.conf_99.txt", package = "maftools")
scores.gistic <- system.file("extdata", "scores.gistic", package = "maftools")
laml.gistic = readGistic(gisticAllLesionsFile = all.lesions, gisticAmpGenesFile = amp.genes, gisticDelGenesFile = del.genes, gisticScoresFile = scores.gistic)
getCytobandSummary(laml.gistic)

Example output

-Processing Gistic files..
--Processing amp_genes.conf_99.txt
--Processing del_genes.conf_99.txt
--Processing scores.gistic
--Summarizing by samples
       Unique_Name nGenes nSamples Variant_Classification Cytoband
 1:   AP_2:11q23.3      1       17                    Amp  11q23.3
 2:    DP_2:5q31.2    377       18                    Del   5q31.2
 3:   AP_4:21q22.2     18       14                    Amp  21q22.2
 4:    DP_4:7q32.3    299       23                    Del   7q32.3
 5:  DP_10:17q11.2     14       13                    Del  17q11.2
 6:    DP_3:7p12.1      1       16                    Del   7p12.1
 7:   DP_8:16q23.1    294        9                    Del  16q23.1
 8:   DP_6:12p13.2     28       10                    Del  12p13.2
 9:      DP_1:3p13     42        8                    Del     3p13
10: DP_11:18p11.21     12        9                    Del 18p11.21
11:      AP_1:1p33      2        7                    Amp     1p33
12:  DP_7:12q21.33     47        3                    Del 12q21.33
13:   DP_9:17p13.2    203       15                    Del  17p13.2
14: DP_12:20q13.13    288        4                    Del 20q13.13
15:  AP_3:20q11.21     35        3                    Amp 20q11.21
16:   DP_5:9q21.32    963        5                    Del  9q21.32
             Wide_Peak_Limits    qvalues
 1: chr11:118341650-118354357 1.1450e-08
 2:  chr5:112352080-156195999 1.2971e-07
 3:   chr21:39509205-42282190 7.0827e-07
 4:  chr7:126055410-159138663 3.4101e-05
 5:   chr17:28936804-29722618 3.2380e-04
 6:    chr7:50632522-51004541 7.8337e-04
 7:   chr16:66750041-90354753 1.0312e-03
 8:   chr12:11415451-13714180 2.3827e-03
 9:    chr3:64670406-75960297 2.0059e-02
10:   chr18:12273033-13664017 2.0884e-02
11:    chr1:47516423-47533836 2.5106e-02
12:   chr12:88430194-96043393 9.7556e-02
13:           chr17:1-7744654 1.2511e-01
14:   chr20:30824328-55265903 1.4746e-01
15:   chr20:26197900-30867110 1.8592e-01
16:          chr9:1-141213431 2.4147e-01

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