{"id":660,"date":"2025-12-04T19:36:26","date_gmt":"2025-12-04T11:36:26","guid":{"rendered":"https:\/\/www.kz-hub.tech\/?p=660"},"modified":"2025-12-04T19:42:30","modified_gmt":"2025-12-04T11:42:30","slug":"absolute%e5%ae%89%e8%a3%85","status":"publish","type":"post","link":"https:\/\/www.kz-hub.tech\/index.php\/2025\/12\/04\/absolute%e5%ae%89%e8%a3%85\/","title":{"rendered":"ABSOLUTE\u5b89\u88c5\u4e0e\u4f7f\u7528"},"content":{"rendered":"

\u5b89\u88c5\u53c2\u8003\uff1a
\nhttps:\/\/geekdaxue.co\/read\/biotrainee@wes\/rrwrli#fghc8w<\/a>
\nhttps:\/\/github.com\/SiYangming\/HAPSEG<\/a><\/p>\n

ABSOLUTE\u4e0b\u8f7d\u5730\u5740\uff1ahttps:\/\/github.com\/Yunuuuu\/ABSOLUTE\/blob\/main\/ABSOLUTE_1.0.6.tar.gz<\/a>
\nHAPSEG\u4e0b\u8f7d\u5730\u5740\uff1ahttps:\/\/github.com\/SiYangming\/HAPSEG\/releases<\/a><\/p>\n

## \u9996\u5148\u9700\u8981\u5148\u5b89\u88c5\u4f9d\u8d56\u5305\ninstall.packages(c("numDeriv","Cairo","RGtk2","cairoDevice"))\nBiocManager::install(c("DNAcopy", "geneplotter", "DNAcopy", "Rcpp", "numDeriv", "foreach"))\n\n## \u518d\u5b89\u88c5\u4e24\u4e2aR\u5305\ninstall.packages("HAPSEG_1.1.1.tar.gz",repos=NULL)\ninstall.packages("ABSOLUTE_1.0.6.tar.gz",repos=NULL)<\/code><\/pre>\n
\u4f7f\u7528\uff1a<\/p>\n
## \u6d4b\u8bd5\uff0c\u4e00\u822c\u53c2\u6570\u4f7f\u7528\u9ed8\u8ba4\u53c2\u6570\uff0c\u8fd9\u91cc\u4f7f\u7528\u7684\u662f\u4e0a\u9762\u94fe\u63a5\u7684\u63a8\u8350\u53c2\u6570\nRunAbsolute(\n    seg.dat.fn = "SNP6_solid_tumor.seg.txt", \n    sigma.p = 0,\n    max.sigma.h = 0.2,\n    min.ploidy = 0.5, \n    max.ploidy = 8, \n    primary.disease = "BLCA", \n    platform = "SNP_6.0", \n    results.dir = "solid", \n    sample.name = "solid", \n    max.as.seg.count = 1500, \n    max.neg.genome = 0.005\n    max.non.clonal = 1, \n    copy_num_type = "total", \n    maf.fn = "solid_tumor.maf.txt",\n    min.mut.af = 0.1\n)<\/code><\/pre>\n
\u8f93\u5165\u6587\u4ef6\u683c\u5f0f\u8981\u6c42\uff1a<\/h2>\n
segments \u6587\u4ef6\uff1a<\/h3>\n
file in either of the following two formats:<\/p>\n
    \n
  1. For ALLELIC copy number type analysis, supply an RData file produced by HAPSEG or AllelicCapseg. These datasets allow incorporation of copy neutral LOH events. Segmentation data produced by any other means must conform to the output formats of HAPSEG\/AllelicCapseg for ABSOLUTE to consider copy neutral LOH events.<\/li>\n
  2. For TOTAL copy number type analysis, suppy a tab-delimited segmentation file in plain-text format. File extension does not matter. ABSOLUTE algorithm v1.0.6 requires the following five columns. Additional columns are ignored.\n
      \n
    • Chromosome<\/li>\n
    • In either chr# or # format.<\/li>\n
    • Start<\/li>\n
    • End<\/li>\n
    • Num_Probes<\/li>\n
    • Segment_Mean<\/li>\n<\/ul>\n<\/li>\n<\/ol>\n
      maf \u6587\u4ef6\uff1a<\/h2>\n
      (Optional) Somatic mutation data in mutation annotation format (MAF) and as a plain text file. File extension does not matter and hashtagged header rows (#) may be present. ABSOLUTE algorithm v1.0.6 requires the following seven columns. Additional columns are ignored.<\/p>\n
        \n
      1. t_ref_count OR i_t_ref_count
        \nCount of reference alleles in tumor.<\/li>\n
      2. t_alt_count OR i_t_alt_count
        \nCount of alternate alleles in tumor. Together with t_ref_count adds up to the depth of reads in the tumor BAM alignment. You can calculate a missing value if two of these three values are known or with read depth and the frequency of the alternate allele within the sample. These and other MuTect output columns are described further in the GATK forum.<\/li>\n
      3. dbSNP_Val_Status
        \nFields may be blank and multiple values are separated with nonspaced semicolon. Example values include bySubmitter, by1000genomes, by2Hit2Allele, and byHapMap.<\/li>\n
      4. Start_position
        \nNote the lowercase \u201cp\u201d. Also, note that the End_position column is not required. This implies that ABSOLUTE algorithm v1.0.6 treats all mutation data equally as point mutations, the expected type of mutation data.<\/li>\n
      5. Tumor_Sample_Barcode
        \nFields may be blank.<\/li>\n
      6. Hugo_Symbol
        \nFields may be blank or \u201cunknown\u201d.<\/li>\n
      7. Chromosome
        \nMust be in # format and not chr# format. The # value must correspond to that in the segmented copy ratios data file identically. For example, ABSOLUTE does not equate X with 23 and will exclude these mutations as unmapped mutations. Note ABSOLUTE algorithm v1.0.6 excludes X chromosome data but not numbered chromosome, e.g. chr23, data.<\/li>\n<\/ol>\n","protected":false},"excerpt":{"rendered":"
        \u5b89\u88c5\u53c2\u8003\uff1a https:\/\/geekdaxue.co\/read\/biotrainee@wes\/rrwrli#f…<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[1],"tags":[],"class_list":["post-660","post","type-post","status-publish","format-standard","hentry","category-uncategorized"],"_links":{"self":[{"href":"https:\/\/www.kz-hub.tech\/index.php\/wp-json\/wp\/v2\/posts\/660","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.kz-hub.tech\/index.php\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.kz-hub.tech\/index.php\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.kz-hub.tech\/index.php\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/www.kz-hub.tech\/index.php\/wp-json\/wp\/v2\/comments?post=660"}],"version-history":[{"count":2,"href":"https:\/\/www.kz-hub.tech\/index.php\/wp-json\/wp\/v2\/posts\/660\/revisions"}],"predecessor-version":[{"id":662,"href":"https:\/\/www.kz-hub.tech\/index.php\/wp-json\/wp\/v2\/posts\/660\/revisions\/662"}],"wp:attachment":[{"href":"https:\/\/www.kz-hub.tech\/index.php\/wp-json\/wp\/v2\/media?parent=660"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.kz-hub.tech\/index.php\/wp-json\/wp\/v2\/categories?post=660"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.kz-hub.tech\/index.php\/wp-json\/wp\/v2\/tags?post=660"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}