## ----loadKnitr, echo=FALSE---------------------------------------------------- # library("knitr") # opts_chunk$set(eval=FALSE) library(pander) panderOptions("digits", 3) ## ----eval=FALSE--------------------------------------------------------------- # param = ramwasParameters( # dirproject = ".", # dirbam = "bams", # filebamlist = "bam_list.txt", # filecpgset = "Simulated_chromosome.rds", # cputhreads = 2, # scoretag = "MAPQ", # minscore = 4, # minfragmentsize = 50, # maxfragmentsize = 250, # filecovariates = "covariates.txt", # modelcovariates = NULL, # modeloutcome = "age", # modelPCs = 0, # toppvthreshold = 1e-5, # cvnfolds = 10, # mmalpha = 0, # mmncpgs = c(5, 10, 50, 100, 500, 1000, 5000, 10000) # ) ## ----eval=FALSE--------------------------------------------------------------- # ### R parameter file # dirbam = "/ramwas_project/bams/" # dirproject = "/ramwas_project/" # filebamlist = "/ramwas_project/000_list_of_files.txt" # scoretag = "AS" # minscore = 100 # # ### platform dependent part # if(.Platform$OS.type == "windows"){ # filecpgset="C:/RaMWAS/CpG_set/cpgset_hg19_SNPS_at_MAF_0.05.rds" # } else { # filecpgset="/computing_cluster/ramwas/cpgset_hg19_SNPS_at_MAF_0.05.rds" # } ## ----bam2sample--------------------------------------------------------------- bam2sample = list( sample1 = c("bam1","bam2","bam3"), sample2 = "sample2" ) ## ----CpGsetExample------------------------------------------------------------ cpgset = list( chr1 = c(12L, 57L, 123L), chr2 = c(45L, 95L, 99L, 111L), chr3 = c(22L, 40L, 199L, 211L) ) ## ----marts, eval=FALSE-------------------------------------------------------- # library(biomaRt) # library(ramwas) # # # First pick a host. # bihost = "grch37.ensembl.org" # # # First we list databases # listOfMarts = listMarts(host = bihost) # pander(head(listOfMarts, 10)) # # # Pick a database # bimart = "ENSEMBL_MART_ENSEMBL" # # # Connect to the database # mart = useMart(biomart = bimart, host = bihost) # # # List the data sets in the database # listOfDatasets = listDatasets(mart = mart) # pander(head(listOfDatasets, 10)) # # # Pisk a data set # bidataset = "hsapiens_gene_ensembl" # # # Connect to the data set # mart = useMart(biomart = bimart, dataset = bidataset, host = bihost) # # # List the attributes # listOfAttributes = listAttributes(mart) # pander(head(listOfAttributes, 10)) # # # Pick attributes # biattributes = c("hgnc_symbol", "entrezgene", "strand") # # listOfFilters = listFilters(mart) # pander(head(listOfFilters, 20)) # # # Pick a filter # bifilters = list(with_hgnc_trans_name=TRUE) # # # Test a location # chr = "chr1" # pos = 15975530 # param = ramwasParameters( # bihost = bihost, # bimart = bimart, # bidataset = bidataset, # biattributes = biattributes, # bifilters = bifilters, # biflank = 0) # # anno = ramwasAnnotateLocations(param, chr, pos) # pander(anno)