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This article introduces the relevant knowledge of "how to use maf_oncoplot.r of R language". In the operation process of actual cases, many people will encounter such difficulties. Next, let Xiaobian lead you to learn how to deal with these situations! I hope you can read carefully and learn something!

maf_oncoplot.r Mutation Comment File Classification Visualization maftools

Usage:Rscript /share/nas1/zhangll/MAF/code/maf_oncoplot.r -usage: /share/nas1/zhangll/MAF/code/maf_oncoplot.r [-h] -i maffle-m metadata -g group [-a additive [additive ...]] [-T topgene] [-l genelist [genelist ...]] [-t] [-o outdir] [-H height] [-W width]Mutation annotation file classificationvisualization:https://www.. com/article/1518optional arguments: -h, --help show this help message and exit -i maffile, --maf maffile input the maf file[required] -m metadata, --meta metadata input metadata file path[required] -g group, --group group input group id in metadata file to classification visualization[required] -a additive [additive ...], --additive additive [additive ...] add additional class[optional,default: NULL] -T topgene, --top topgene Number of top genes displayed [optional, default: 20] -l genelist [genelist ...], --genelist genelist [genelist ...] the selected gene list to display [optional, default: NULL] -t, --showtitle whether show maftools title of plot [optional, default: False] -o outdir, --outdir outdir output file directory [default cwd] -H height, --height height the height of pic inches [default 8] -W width, --width width the width of pic inches [default 8] Parameter description:

-i Path to mutation annotation file maf, which can be downloaded directly from TCGA database:

Hugo_Symbol

Entrez_Gene_Id

Center

NCBI_Build

Chromosome

Start_Position

End_Position

Strand

Variant_Classification

MFN2

9927

WUGSC

GRCh48

chr1

1200177712001777

+

Missense_Mutation

KCNG3

170850

WUGSC

GRCh48

chr2

4244457842444578

+Missense_Mutation

MAP2

4133WUGSCGRCh48

chr2

209692762

209692762

+

Missense_Mutation

HEG1

57493

WUGSC

GRCh48

chr3

125010546

125010546

+

Missense_Mutation

PCDHB11

56125

WUGSC

GRCh48

chr5

141200541141200541

+

Missense_Mutation

NSD1

64324

WUGSC

GRCh48

chr5

177294257177294257

+

Missense_Mutation

F13A1

2162WUGSCGRCh48

chr6

61746096174609

+

Missense_Mutation

PRRT4

401399

WUGSCGRCh48

chr7

128359624128359624

+

Missense_Mutation

FBP2

8789

WUGSCGRCh48

chr9

94558941

94558941

+

Missense_Mutation

-m metadata file, all kinds of characteristic information of patient sample, must contain the column of patient TCGA number named by patient:

patient

sample

shortLetterCode

tumor_stagetissue_or_organ_of_origin

alcohol_history

gender

ethnicity

race

TCGA-M9-A5M8

TCGA-M9-A5M8-01A

TP

stage iia

Lower third of esophagus

Yes

male

not reported

not reported

TCGA-R6-A6DQ

TCGA-R6-A6DQ-01B

TP

not reported

Lower third of esophagus

Yes

female

not hispanic or latino

white

TCGA-LN-A9FP

TCGA-LN-A9FP-01A

TP

stage iiaMiddle third of esophagus

Yes

female

not hispanic or latino

asian

TCGA-LN-A4MQ

TCGA-LN-A4MQ-01A

TP

stage iii

Lower third of esophagus

No

male

not hispanic or latino

asian

TCGA-JY-A93D

TCGA-JY-A93D-01A

TP

stage iiic

Lower third of esophagus

Yes

male

not reported

white

TCGA-IG-A3YB

TCGA-IG-A3YB-01A

TP

stage iiia

Lower third of esophagus

No

male

not hispanic or latino

white

TCGA-IC-A6RF

TCGA-IC-A6RF-01A

TP

stage ia

Middle third of esophagus

Yes

female

not hispanic or latino

white

TCGA-VR-A8EX

TCGA-VR-A8EX-01A

TP

stage iva

Middle third of esophagus

No

male

not reported

not reported

-g Specifies the metadata group column name. If the group name has spaces, it should be enclosed in quotation marks.

-a Additional grouping column names, the results will be shown in the figure

-T Specifies the number of top genes to be displayed, default 20

-l Specify the list of genes to be displayed, separated by spaces, default NULL

Examples of use: Rscript /share/nas1/zhangll/MAF/code/maf_oncoplot.r -i /share/nas1/zhangll/MAF/TCGA-ESCA.maf_maftools.maf -m /share/nas1/huangls/project/TCGA_ESCA/metadata.tsv -g gender"How to use maf_oncoplot.r in R language" is introduced here. Thank you for reading it. If you want to know more about industry-related knowledge, you can pay attention to the website. Xiaobian will output more high-quality practical articles for everyone!

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