b.limour.top/source/_posts/cbioportal的原始数据获取.md

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title: cBioPortal的原始数据获取 tags: [] id: '1680' categories:

• - 组织测序分析 date: 2022-02-18 11:02:21 ---

cBioPortal中的文章相关数据都存放在这里：https://github.com/cBioPortal/datahub/tree/master/public

第一步 获取需要的数据

wget https://github.com/cBioPortal/datahub/raw/master/public/prad_su2c_2019/data_mrna_seq_fpkm_capture.txt

第二步 读取数据

f_name_dedup <- function(lc_exp, rowN = 1){
    res <- lc_exp[-rowN]
    lc_tmp = by(res,
         lc_exp[[rowN]],
         function(x) rownames(x)[which.max(rowMeans(x))])
    lc_probes = as.character(lc_tmp)
    res = lc_exp[rownames(res) %in% lc_probes,]
    rownames(res) <- res[[rowN]]
    res[-rowN]
}

d <- read.table('data_mrna_seq_fpkm_capture.txt', header = T, sep = '\t', allowEscapes = T)
d <- f_name_dedup(d)
d <- d[,order(colnames(d))]

第三步 导出需要的基因

write.csv(t(log1p(d[c('RPLP0', 'GAPDH'),])), file='prad_su2c_2019.csv.csv')