germVar2:TCGA种系变体

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  • 2022-05-25 05:55
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胚芽2 补充材料 泛癌测序分析显示癌症基因中频繁发生种系突变 姜若木,威廉·李,纳德姆·里亚兹,克里斯·桑德,蒂莫西·米奇森^ ,黛博拉·S·马克斯^ 安装 install.packages("devtools") library(devtools) install_github("rj67/germVar2") 数据对象 可以加载的数据框 list_goi-候选基因列表 基因 批准名称 合奏基因 千年发展目标 CPG 班级 83 自动取款机 ATM丝氨酸/苏氨酸激酶 ENSG00000149311 真的 真的 时差 135 BRCA1 乳腺癌1,早发 ENSG00000012048 真的 真的 时差 all_patients-所有患者信息 病人 疾病2 年龄 Agez EA 种族2 性别 P6-A5OG 行政协调会 45 -0.2248333 真的 白色的
germVar2-master.zip
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germVar2 ============= Supplementary materials for #### Pan-cancer sequencing analysis reveals frequent germline mutations in cancer genes Ruomu Jiang, William Lee, Nadeem Riaz, Chris Sander, Timothy J Mitchison^*, Debora S Marks^* Install ----------- install.packages("devtools") library(devtools) install_github("rj67/germVar2") Data objects ----------- Dataframes that can be loaded * list_goi -- candidate gene list | |Gene |Approved.Name |Ensembl.Gene |MDG |CPG |Class | |:---|:-----|:----------------------------|:---------------|:----|:----|:-----| |83 |ATM |ATM serine/threonine kinase |ENSG00000149311 |TRUE |TRUE |H-TSG | |135 |BRCA1 |breast cancer 1, early onset |ENSG00000012048 |TRUE |TRUE |H-TSG | * all_patients -- all the patient information |Patient |disease2 | age| agez|EA |race2 |gender | |:-------|:--------|---:|----------:|:----|:-----|:------| |P6-A5OG |ACC | 45| -0.2248333|TRUE |WHITE |FEMALE | |OR-A5JY |ACC | 68| 1.0679583|TRUE |WHITE |FEMALE | * LoF_vars -- variant information, each row is a variant and columns are various annotation | |Gene |uid |EFF | TAC2| AN2|rare |AAChange |Transcript | |:----|:-----|:----------------|:------------------|----:|-----:|:----|:----------------------|:---------------| |3444 |BRCA1 |17-41199682-C-T |stop_gained | 1| 17630|TRUE |p.Trp711*/c.2133G>A |ENST00000491747 | |3445 |BRCA1 |17-41201208-TG-T |frameshift_variant | 1| 17630|TRUE |p.Gln1732fs/c.5194delC |ENST00000493795 | * LoF_muts -- variant carrier information, each row corresponds to the carrier of a particular variant. | |Gene |uid |Patient |disease2 |AAChange | DP| AB|N_hom | nA| nB| |:---|:-----|:----------------|:-------|:--------|:----------------------|--:|---------:|:-----|--:|--:| |8 |BRCA1 |17-41247941-T-G |04-1336 |OV |c.453A>C | 39| 0.9411765|FALSE | 3| 0| |205 |BRCA1 |17-41201208-TG-T |09-2045 |OV |p.Gln1732fs/c.5194delC | 96| 0.8541667|FALSE | 1| 0| * nsSNP_vars -- variant information, each row is a variant and columns are various annotation | |Gene |uid |EFF | TAC2| AN2|rare |AAChange |Transcript |dele |RCVaccession | cosm_scount| |:---------------|:-----|:---------------|:----------------|----:|-----:|:----|:----------------------|:---------------|:-----|:-------------------------|-----------:| |17-41201181-C-A |BRCA1 |17-41201181-C-A |missense_variant | 1| 17630|TRUE |p.Gly1788Val/c.5363G>T |ENST00000357654 |TRUE |RCV000048961;RCV000031241 | NA| |17-41215920-G-A |BRCA1 |17-41215920-G-A |missense_variant | 1| 17630|TRUE |p.Ala1708Val/c.5123C>T |ENST00000357654 |FALSE |NA | NA| * nsSNP_muts -- variant carrier information, each row corresponds to the carrier of a particular variant. | |Gene |uid |Patient |disease2 |AAChange | DP| AB|N_hom | nA| nB| |:--|:-----|:---------------|:-------|:--------|:---------------------|---:|---------:|:-----|--:|--:| |3 |BRCA1 |17-41245027-G-A |02-0047 |GBM |p.Arg841Trp/c.2521C>T | 330| 0.4575758|FALSE | 1| 1| |89 |BRCA1 |17-41245027-G-A |05-5425 |LUAD |p.Arg841Trp/c.2521C>T | 195| 0.5179487|FALSE | 3| 1| Juptyer notebooks ----------- Reproduce most of the analysis/figures in the paper * project_overview -- Samples, candidate gene, all variants overview. * known_cancer_gene_variants -- Summary variants in known cancer genes. * loss_of_heterozygousity_analysis -- LOH of all germline variants * low_frequency_variants_association -- Assocation test of low frequency missense and truncation variants comparing to 1000G and ESP Convenience functions ----------- * plotMutRNASeq -- Plot mutation RNASeq levels * plotDiseaseDistr -- Plot cancer type distribution given a list of mutations Dependency ----------- * plyr, dplyr, reshape2, ggplot2, magrittr, RColorbrewer, gridExtra
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