## ----- loadknitr，echo = false ------------------------------------------------------------------------------------------------------------------------------------------------＃library（“ knitr”）＃opts_chunk $ set（eval = false）库（pander）panderoptions（“ digits”，3）## ------------------------------------------------------------------------------------------------------------------ # 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，＃null，＃modelout commitecom= 0，＃toppvthreshold = 1e-5，＃cvnfolds = 10，＃mmalpha = 0，＃mmncpgs = c（5、10、50、100、500、500、1000、5000、10000）＃= ----------------------------------------------------------------------------------------------------------------------------------------------------------- # ### R parameter file # dirbam = "/ramwas_project/bams/" # dirproject = "/ramwas_project/" # filebamlist = "/ramwas_project/000_list_of_files.txt“＃scoretag =” as“＃minScore = 100＃###平台dedemt＃if（.platform $ os.type ==“ Windows”）{＃Filecpgset =“ C：/ramwas/cpg_set/cpgset/cpgset_hg19_snps_at_at_maf_0.0.05.rds”＃05.rds“＃} ## ---- BAM2Sample -------------------------------------------------------------------------------------------------------------- bam2sample = list( sample1 = c("bam1","bam2","bam3"), sample2 = "示例2“）## --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 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)