Removed 7 duplicated variants
2022-02-18 本文已影响0人
PhageNanoenzyme
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> # laml = read.maf(maf = laml.maf, clinicalData = laml.clin)
> # laml
> # laml@data
> # laml@summary
> # laml@variants.per.sample
> # laml@variant.type.summary
> # laml@variant.classification.summary
> # laml@gene.summary
> # laml@maf.silent
> # laml@clinical.data
> library(maftools)
> #修改为tab键分割的文件
> #突变文件
> laml.maf <- './NGS23_0.maf.gz'
> laml.maf
[1] "./NGS23_0.maf.gz"
> laml = read.maf(maf = laml.maf)
-Reading
-Validating
Error in validateMaf(maf = maf, isTCGA = isTCGA, rdup = removeDuplicatedVariants, :
missing required fields from MAF: Tumor_Sample_Barcode
> # laml = read.maf(maf = laml.maf, clinicalData = laml.clin)
> # laml
> # laml@data
> # laml@summary
> # laml@variants.per.sample
> # laml@variant.type.summary
> # laml@variant.classification.summary
> # laml@gene.summary
> # laml@maf.silent
> # laml@clinical.data
> library(maftools)
> #修改为tab键分割的文件
> #突变文件
> laml.maf <- './NGS23_0.maf.gz'
> laml.maf
[1] "./NGS23_0.maf.gz"
> laml = read.maf(maf = laml.maf)
-Reading
-Validating
Error in validateMaf(maf = maf, isTCGA = isTCGA, rdup = removeDuplicatedVariants, :
missing required fields from MAF: Chromosome
> # laml = read.maf(maf = laml.maf, clinicalData = laml.clin)
> # laml
> # laml@data
> # laml@summary
> # laml@variants.per.sample
> # laml@variant.type.summary
> # laml@variant.classification.summary
> # laml@gene.summary
> # laml@maf.silent
> # laml@clinical.data
> library(maftools)
> #修改为tab键分割的文件
> #突变文件
> laml.maf <- './exp_23.maf.gz'
> laml.maf
[1] "./exp_23.maf.gz"
> laml = read.maf(maf = laml.maf)
-Reading
-Validating
--Removed 7 duplicated variants
--Non MAF specific values in Variant_Type column:
INT
-Summarizing
--Possible FLAGS among top ten genes:
MUC5B
-Processing clinical data
--Missing clinical data
-Finished in 7.280s elapsed (0.850s cpu)
> # laml = read.maf(maf = laml.maf, clinicalData = laml.clin)
> # laml
> # laml@data
> # laml@summary
> # laml@variants.per.sample
> # laml@variant.type.summary
> # laml@variant.classification.summary
> # laml@gene.summary
> # laml@maf.silent
> # laml@clinical.data
> library(maftools)
> #修改为tab键分割的文件
> #突变文件
> laml.maf <- './exp_23.maf.gz'
> laml.maf
[1] "./exp_23.maf.gz"
> laml = read.maf(maf = laml.maf)
-Reading
-Validating
--Removed 7 duplicated variants
-Summarizing
--Possible FLAGS among top ten genes:
MUC5B
-Processing clinical data
--Missing clinical data
-Finished in 7.120s elapsed (1.410s cpu)
> #Shows sample summry.
> getSampleSummary(laml)
Tumor_Sample_Barcode Frame_Shift_Del Frame_Shift_Ins In_Frame_Del In_Frame_Ins
1: 19O024962 1 2 1 0
2: 20O032721 0 0 1 0
3: 20O036851 1 0 0 0
4: 20O036854 0 1 0 0
5: 19O024975 1 0 3 0
6: 19O025542 2 2 0 0
7: 21O041199 1 0 0 1
8: 20O030287 0 1 0 0
9: 19O009587 0 0 1 0
10: 19O024947 1 0 0 0
11: 19O014350 0 1 0 0
12: 19O014357 0 0 0 0
13: 19O024953 0 0 0 0
14: 19O007952 1 0 0 0
15: 20O032274 0 1 1 0
16: 19O024236 0 0 0 1
17: 20O026723 0 0 0 0
18: 20O036858 0 0 0 0
19: 20O038833 1 0 0 0
20: 19O024882 0 0 0 0
21: 20O036856 0 1 0 0
22: 20O036868 0 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: 34 2 6 46
2: 18 1 0 20
3: 12 0 0 13
4: 10 1 1 13
5: 3 1 2 10
6: 4 1 0 9
7: 6 0 0 8
8: 6 0 0 7
9: 4 1 0 6
10: 4 1 0 6
11: 3 1 0 5
12: 3 1 1 5
13: 5 0 0 5
14: 0 2 0 3
15: 1 0 0 3
16: 0 0 1 2
17: 2 0 0 2
18: 1 1 0 2
19: 1 0 0 2
20: 1 0 0 1
21: 0 0 0 1
22: 1 0 0 1
Missense_Mutation Nonsense_Mutation Splice_Site total
> #Shows gene summary.
> getGeneSummary(laml)
Hugo_Symbol Frame_Shift_Del Frame_Shift_Ins In_Frame_Del In_Frame_Ins Missense_Mutation
1: TP53 2 0 1 0 1
2: MUC5B 0 0 0 0 5
3: CREBBP 1 0 0 0 1
4: EGFR 0 0 0 2 0
5: HRAS 0 0 0 0 2
---
144: ZC3H6 0 0 0 0 1
145: ZDHHC4 0 0 0 0 1
146: ZNF703 0 0 0 0 1
147: ZNRF3 0 0 0 0 0
148: ZSCAN5A 0 0 0 0 1
Nonsense_Mutation Splice_Site total MutatedSamples AlteredSamples
1: 2 0 6 5 5
2: 0 0 5 4 4
3: 0 0 2 2 2
4: 0 0 2 2 2
5: 0 0 2 2 2
---
144: 0 0 1 1 1
145: 0 0 1 1 1
146: 0 0 1 1 1
147: 1 0 1 1 1
148: 0 0 1 1 1
> #Shows all fields in MAF
> getFields(laml)
[1] "Hugo_Symbol" "Entrez_Gene_Id" "Center"
[4] "NCBI_Build" "Chromosome" "Start_Position"
[7] "End_Position" "Strand" "Variant_Classification"
[10] "Variant_Type" "Reference_Allele" "Tumor_Seq_Allele1"
[13] "Tumor_Seq_Allele2" "Tumor_Sample_Barcode" "Protein_Change"
[16] "i_TumorVAF_WU" "i_transcript_name"
> #shows clinical data associated with samples
> getClinicalData(laml)
Tumor_Sample_Barcode
1: 19O007952
2: 19O009587
3: 19O014350
4: 19O014357
5: 19O024236
6: 19O024882
7: 19O024947
8: 19O024953
9: 19O024962
10: 19O024975
11: 19O025542
12: 20O026723
13: 20O030287
14: 20O032274
15: 20O032721
16: 20O036851
17: 20O036854
18: 20O036856
19: 20O036858
20: 20O036868
21: 20O038833
22: 21O041199
Tumor_Sample_Barcode
> #Writes maf summary to an output file with basename laml.
> #write.mafSummary(maf = laml, basename = 'laml')
> #plotmafSummary
> plotmafSummary(maf = laml, rmOutlier = TRUE, addStat = 'median', dashboard = TRUE, titvRaw = FALSE)
