## ----setup, message=FALSE, warning=FALSE-------------------------------------- library(maftools) ## ----eval=FALSE--------------------------------------------------------------- # can_hs_tbl = maftools::cancerhotspots( # bam = "Tumor.bam", # refbuild = "GRCh37", # mapq = 10, # sam_flag = 1024 # ) ## ----eval=FALSE--------------------------------------------------------------- # head(can_hs_tbl) # # # loci fa_ref NT_change Hugo_Symbol Variant_Classification AA_change Meta VAF A T G C Ins Del # # 1: 1:2491289 NA G>A TNFRSF14 Missense_Mutation C111Y deleterious(0) 0 0 0 21 0 0 0 # # 2: 1:2491290 NA C>G TNFRSF14 Missense_Mutation C111W deleterious(0) 0 0 0 0 21 0 0 # # 3: 1:8073432 NA T>G ERRFI1 Missense_Mutation K409N deleterious(0) 0 1 64 0 1 0 0 # # 4: 1:8073434 NA T>G ERRFI1 Missense_Mutation K409Q deleterious(0.04) 0 0 63 0 0 0 0 # # 5: 1:8074313 NA T>A ERRFI1 Nonsense_Mutation K116* 0 0 106 0 0 0 0 # # 6: 1:9779982 NA T>C PIK3CD Missense_Mutation C416R tolerated(0.26) 0 1 18 0 0 0 0 ## ----------------------------------------------------------------------------- #Generate a sample loci - first two columns must contain chromosome name and position loci = data.table::data.table(chr = c("seq1", "seq2"), pos = c(1340, 1483)) loci ## ----eval=FALSE--------------------------------------------------------------- # #Example BAM file from Rsamtools package # #By default position are assumed to be in 1-based coordinate system # bamfile = system.file("extdata", "ex1.bam", package = "Rsamtools") # loci_rc = maftools::bamreadcounts(bam = bamfile, loci = loci) # # loci_rc # # $ex1 # # loci fa_ref A T G C Ins Del # # 1: seq1:1340 NA 1 0 0 62 0 0 # # 2: seq2:1483 NA 0 13 0 0 0 0 ## ----------------------------------------------------------------------------- sessionInfo()