R관련 썸네일형 리스트형 GSEA Enrichment Score calculation #' Calculate Enrichment score for GSEA plot#' #' This function is slightly modified from GSEA.1.0.R downloaded from msigDB.\cr#' Specific site address is below.\cr#' http://software.broadinstitute.org/gsea/msigdb/download_file.jsp?filePath=/resources/software/GSEA-P-R.1.0.zip\cr#' Original functions name are 'GSEA.EnrichmentScore' and 'GSEA.GeneRanking'\cr#' I combined two functions into single .. 더보기 GSEA enrichment plot #' Calculate Enrichment score for GSEA plot#' #' This function is slightly modified from GSEA.1.0.R downloaded from msigDB.\cr#' Specific site address is below.\cr#' http://software.broadinstitute.org/gsea/msigdb/download_file.jsp?filePath=/resources/software/GSEA-P-R.1.0.zip\cr#' Original functions name are 'GSEA.EnrichmentScore' and 'GSEA.GeneRanking'\cr#' I combined two functions into single .. 더보기 Rentrez package update symbol and get entrezID #' Update_EntrezID_Officialsymbol_From_Symbol #' #' This function is to get official symbol and entrezid using rentrez #' For more information, please visit https://blog.naver.com/hyosil7979/220857307890 #' @param symbol (default=NULL) : symbol #' @keywords genesymbol, entrez, official genesymbol, conversion #' @export #' @examples #' Update_EntrezID_Officialsymbol_From_Symbol('P53') Update_Entr.. 더보기 calculate GSEA Enrichment score GSEA에서 enrichment plot을 그릴 때 문제는 내가 원하는 그림만 특정해서 그리는 것과 pdf작업하기 불편해서 내가 직접 만듬원본 GSEA R function에서는 signal2Noise 계산 전에 expression value들에 굉장히 작은 값 10E-6을 더하는데 나는 그것을 사용하지 않았고나머지 방식은 모두 동일하게 함. #' Calculate Enrichment score for GSEA plot#' #' This function is slightly modified from GSEA.1.0.R downloaded from msigDB.\cr#' Specific site address is below.\cr#' http://software.broadinstitute.org/gsea/.. 더보기 Color scale bar function color.scaleBAR 더보기 proportion test The two-proportions z-test is used to compare two observed proportions. This article describes the basics of two-proportions *z-test and provides pratical examples using R sfoftware -Proteogenomic characterization of human EOGC _cancercell 2019 For the seven shared significantly mutated genes from TCGA and HK cohorts and MUC5B and BANP from our cohort, we compared nonsynonymous somatic SNV freque.. 더보기 DLL 관련 해결법 maximal number of DLLs reached... 라는 에러 뜨면 해결하는 방법install.packages('usethis')usethis::edit_r_environ() 위의 명령어를 실행하면 R script창이 하나 뜸. 아래를 집어넣음.R_MAX_NUM_DLLS=256기본적으로 DLL은 100이지만 이렇게 하면 256으로 늘어남. 더보기 microarray (affymetrix, illumina) library(limma)exp=read.idat('idat_file_name.idat',bgx_file)#idat_file은 gene expression data#bgx file은 일종의 annotation file임ex2=neqc(exp) # Background intensity correction. https://bioconductor.org/packages/devel/data/experiment/vignettes/BeadArrayUseCases/inst/doc/BeadArrayUseCases.pdfhttps://support.bioconductor.org/p/78325/ 더보기 이전 1 2 3 4 5 ··· 8 다음
