genesToBarcodes: Extracts Tumor Sample Barcodes where the given genes are...
In maftools: Summarize, Analyze and Visualize MAF Files
Description
Usage
Arguments
Value
Examples
View source: R/genesToBarcodes.R
Description
Extracts Tumor Sample Barcodes where the given genes are mutated.
Usage
1
genesToBarcodes(maf, genes = NULL, justNames = FALSE, verbose = TRUE)
Arguments
maf
an MAF object generated by read.maf
genes
Hogo_Symbol for which sample names to be extracted.
justNames
if TRUE, just returns samples names instead of summarized tables.
verbose
Default TRUE
Value
list of data.tables with samples in which given genes are mutated.
Examples
1
2
3
laml.maf <- system.file("extdata", "tcga_laml.maf.gz", package = "maftools")
laml <- read.maf(maf = laml.maf)
genesToBarcodes(maf = laml, genes = 'DNMT3A')
Example output
-Reading
-Validating
-Silent variants: 475
-Summarizing
-Processing clinical data
--Missing clinical data
-Finished in 0.532s elapsed (0.440s cpu)
$DNMT3A
Tumor_Sample_Barcode Frame_Shift_Del Frame_Shift_Ins In_Frame_Del
1: TCGA-AB-2912 0 1 0
2: TCGA-AB-2822 1 0 0
3: TCGA-AB-2839 1 2 0
4: TCGA-AB-2863 0 0 1
5: TCGA-AB-2908 2 0 0
6: TCGA-AB-2938 3 0 0
7: TCGA-AB-2861 0 0 0
8: TCGA-AB-2925 0 0 0
9: TCGA-AB-2949 2 0 0
10: TCGA-AB-2891 0 0 0
11: TCGA-AB-2830 1 1 0
12: TCGA-AB-2864 0 1 0
13: TCGA-AB-2988 0 1 0
14: TCGA-AB-2887 0 0 0
15: TCGA-AB-2898 0 1 1
16: TCGA-AB-2945 1 1 0
17: TCGA-AB-2955 1 0 0
18: TCGA-AB-2968 1 1 0
19: TCGA-AB-2895 0 0 0
20: TCGA-AB-2966 1 0 0
21: TCGA-AB-2993 1 1 0
22: TCGA-AB-2859 2 1 0
23: TCGA-AB-2931 0 0 0
24: TCGA-AB-2965 1 1 0
25: TCGA-AB-2967 0 3 0
26: TCGA-AB-2802 0 2 0
27: TCGA-AB-2867 0 0 0
28: TCGA-AB-2928 1 0 0
29: TCGA-AB-2869 0 1 0
30: TCGA-AB-2916 0 0 0
31: TCGA-AB-2919 0 0 0
32: TCGA-AB-2934 0 1 0
33: TCGA-AB-2818 0 0 0
34: TCGA-AB-2833 0 0 0
35: TCGA-AB-2987 0 1 0
36: TCGA-AB-2851 1 0 0
37: TCGA-AB-2853 0 0 0
38: TCGA-AB-2974 0 1 0
39: TCGA-AB-2816 0 0 0
40: TCGA-AB-2824 0 1 0
41: TCGA-AB-2884 0 1 0
42: TCGA-AB-2981 0 1 0
43: TCGA-AB-2809 0 0 0
44: TCGA-AB-2825 0 1 0
45: TCGA-AB-2896 0 2 0
46: TCGA-AB-2947 0 1 0
47: TCGA-AB-2873 1 0 0
48: TCGA-AB-2975 0 0 0
Tumor_Sample_Barcode Frame_Shift_Del Frame_Shift_Ins In_Frame_Del
In_Frame_Ins Missense_Mutation Nonsense_Mutation Splice_Site total
1: 0 15 1 2 19
2: 0 14 1 1 17
3: 0 13 1 0 17
4: 0 14 1 0 16
5: 0 11 3 0 16
6: 0 13 0 0 16
7: 0 12 1 2 15
8: 1 14 0 0 15
9: 0 12 0 1 15
10: 0 12 0 2 14
11: 1 10 0 0 13
12: 0 10 1 1 13
13: 0 11 0 1 13
14: 0 12 0 0 12
15: 0 8 0 2 12
16: 0 10 0 0 12
17: 1 9 1 0 12
18: 0 8 1 1 12
19: 0 9 0 2 11
20: 0 10 0 0 11
21: 1 6 2 0 11
22: 0 7 0 0 10
23: 0 8 0 2 10
24: 1 7 0 0 10
25: 0 3 2 2 10
26: 0 7 0 0 9
27: 0 8 1 0 9
28: 0 7 1 0 9
29: 1 5 1 0 8
30: 0 6 1 1 8
31: 0 8 0 0 8
32: 1 5 0 1 8
33: 0 5 0 2 7
34: 0 6 1 0 7
35: 0 6 0 0 7
36: 0 4 1 0 6
37: 1 5 0 0 6
38: 0 5 0 0 6
39: 0 5 0 0 5
40: 0 4 0 0 5
41: 0 4 0 0 5
42: 1 2 0 0 4
43: 0 2 1 0 3
44: 0 1 0 1 3
45: 0 1 0 0 3
46: 0 2 0 0 3
47: 0 1 0 0 2
48: 0 1 1 0 2
In_Frame_Ins Missense_Mutation Nonsense_Mutation Splice_Site total
maftools documentation built on Feb. 6, 2021, 2 a.m.
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Description Usage Arguments Value Examples
View source: R/genesToBarcodes.R
Description
Extracts Tumor Sample Barcodes where the given genes are mutated.
Usage
1 | genesToBarcodes(maf, genes = NULL, justNames = FALSE, verbose = TRUE)
|
Arguments
maf |
an |
genes |
Hogo_Symbol for which sample names to be extracted. |
justNames |
if TRUE, just returns samples names instead of summarized tables. |
verbose |
Default TRUE |
Value
list of data.tables with samples in which given genes are mutated.
Examples
1 2 3 | laml.maf <- system.file("extdata", "tcga_laml.maf.gz", package = "maftools")
laml <- read.maf(maf = laml.maf)
genesToBarcodes(maf = laml, genes = 'DNMT3A')
|
Example output
-Reading
-Validating
-Silent variants: 475
-Summarizing
-Processing clinical data
--Missing clinical data
-Finished in 0.532s elapsed (0.440s cpu)
$DNMT3A
Tumor_Sample_Barcode Frame_Shift_Del Frame_Shift_Ins In_Frame_Del
1: TCGA-AB-2912 0 1 0
2: TCGA-AB-2822 1 0 0
3: TCGA-AB-2839 1 2 0
4: TCGA-AB-2863 0 0 1
5: TCGA-AB-2908 2 0 0
6: TCGA-AB-2938 3 0 0
7: TCGA-AB-2861 0 0 0
8: TCGA-AB-2925 0 0 0
9: TCGA-AB-2949 2 0 0
10: TCGA-AB-2891 0 0 0
11: TCGA-AB-2830 1 1 0
12: TCGA-AB-2864 0 1 0
13: TCGA-AB-2988 0 1 0
14: TCGA-AB-2887 0 0 0
15: TCGA-AB-2898 0 1 1
16: TCGA-AB-2945 1 1 0
17: TCGA-AB-2955 1 0 0
18: TCGA-AB-2968 1 1 0
19: TCGA-AB-2895 0 0 0
20: TCGA-AB-2966 1 0 0
21: TCGA-AB-2993 1 1 0
22: TCGA-AB-2859 2 1 0
23: TCGA-AB-2931 0 0 0
24: TCGA-AB-2965 1 1 0
25: TCGA-AB-2967 0 3 0
26: TCGA-AB-2802 0 2 0
27: TCGA-AB-2867 0 0 0
28: TCGA-AB-2928 1 0 0
29: TCGA-AB-2869 0 1 0
30: TCGA-AB-2916 0 0 0
31: TCGA-AB-2919 0 0 0
32: TCGA-AB-2934 0 1 0
33: TCGA-AB-2818 0 0 0
34: TCGA-AB-2833 0 0 0
35: TCGA-AB-2987 0 1 0
36: TCGA-AB-2851 1 0 0
37: TCGA-AB-2853 0 0 0
38: TCGA-AB-2974 0 1 0
39: TCGA-AB-2816 0 0 0
40: TCGA-AB-2824 0 1 0
41: TCGA-AB-2884 0 1 0
42: TCGA-AB-2981 0 1 0
43: TCGA-AB-2809 0 0 0
44: TCGA-AB-2825 0 1 0
45: TCGA-AB-2896 0 2 0
46: TCGA-AB-2947 0 1 0
47: TCGA-AB-2873 1 0 0
48: TCGA-AB-2975 0 0 0
Tumor_Sample_Barcode Frame_Shift_Del Frame_Shift_Ins In_Frame_Del
In_Frame_Ins Missense_Mutation Nonsense_Mutation Splice_Site total
1: 0 15 1 2 19
2: 0 14 1 1 17
3: 0 13 1 0 17
4: 0 14 1 0 16
5: 0 11 3 0 16
6: 0 13 0 0 16
7: 0 12 1 2 15
8: 1 14 0 0 15
9: 0 12 0 1 15
10: 0 12 0 2 14
11: 1 10 0 0 13
12: 0 10 1 1 13
13: 0 11 0 1 13
14: 0 12 0 0 12
15: 0 8 0 2 12
16: 0 10 0 0 12
17: 1 9 1 0 12
18: 0 8 1 1 12
19: 0 9 0 2 11
20: 0 10 0 0 11
21: 1 6 2 0 11
22: 0 7 0 0 10
23: 0 8 0 2 10
24: 1 7 0 0 10
25: 0 3 2 2 10
26: 0 7 0 0 9
27: 0 8 1 0 9
28: 0 7 1 0 9
29: 1 5 1 0 8
30: 0 6 1 1 8
31: 0 8 0 0 8
32: 1 5 0 1 8
33: 0 5 0 2 7
34: 0 6 1 0 7
35: 0 6 0 0 7
36: 0 4 1 0 6
37: 1 5 0 0 6
38: 0 5 0 0 6
39: 0 5 0 0 5
40: 0 4 0 0 5
41: 0 4 0 0 5
42: 1 2 0 0 4
43: 0 2 1 0 3
44: 0 1 0 1 3
45: 0 1 0 0 3
46: 0 2 0 0 3
47: 0 1 0 0 2
48: 0 1 1 0 2
In_Frame_Ins Missense_Mutation Nonsense_Mutation Splice_Site total
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