Enter the body of text here
Code should be placed in three backticks as shown below
library(RIPSeeker)
# Retrieve system files
extdata.dir <- system.file("extdata", package="RIPSeeker")
bamFiles <- list.files(extdata.dir, ".bam$", recursive=TRUE, full.names=TRUE)
bamFiles <- grep("PRC2", bamFiles, value=TRUE)
cNAME <- "SRR039214" # specify control name
# output file directory
outDir <- paste(getwd(), "ripSeek_example", sep="/")
# Parameters setting
binSize <- NULL # automatically determine bin size
minBinSize <- 10000 # min bin size in automatic bin size selection
maxBinSize <- 12000 # max bin size in automatic bin size selection
multicore <- TRUE # use multicore
strandType <- "-" # set strand type to minus strand
biomart <- "ENSEMBL_MART_ENSEMBL" # use archive to get ensembl 65
dataset <- "mmusculus_gene_ensembl" # mouse dataset id name
host <- "may2012.archive.ensembl.org" # use ensembl 65 for annotation
goAnno <- "org.Mm.eg.db"
################ run main function ripSeek to predict RIP ################
seekOut <- ripSeek(bamPath=bamFiles, cNAME=cNAME,
binSize=binSize, minBinSize = minBinSize,
maxBinSize = maxBinSize, strandType=strandType,
outDir=outDir, silentMain=FALSE,
verbose=TRUE, reverseComplement=TRUE, genomeBuild="mm9",
biomart=biomart, host=host,
biomaRt_dataset = dataset,
goAnno = goAnno,
uniqueHit = TRUE, assignMultihits = TRUE,
rerunWithDisambiguatedMultihits = TRUE, multicore=multicore)
# include your problematic code here with any corresponding output
Error in UseMethod("filter_") :
no applicable method for 'filter_' applied to an object of class "c('tbl_SQLiteConnection', 'tbl_dbi', 'tbl_sql', 'tbl_lazy', 'tbl')"
# please also include the results of running the following in an R session
sessionInfo( )
R version 3.6.3 (2020-02-29) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 18363)
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages: [1] grid parallel stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] ChIPpeakAnno_3.20.1 VennDiagram_1.6.20 futile.logger_1.4.3
[4] biomaRt_2.42.1 memoise_2.0.0 RIPSeeker_1.26.0
[7] rtracklayer_1.46.0 GenomicAlignments_1.22.1 Rsamtools_2.2.3
[10] Biostrings_2.54.0 XVector_0.26.0 SummarizedExperiment_1.16.1
[13] DelayedArray_0.12.3 BiocParallel_1.20.1 matrixStats_0.58.0
[16] Biobase_2.46.0 GenomicRanges_1.38.0 GenomeInfoDb_1.22.1
[19] IRanges_2.20.2 S4Vectors_0.24.4 BiocGenerics_0.32.0
loaded via a namespace (and not attached):
[1] ProtGenerics_1.18.0 bitops_1.0-6 bit64_4.0.5 progress_1.2.2
[5] httr_1.4.2 tools_3.6.3 utf8_1.1.4 R6_2.5.0
[9] DBI_1.1.1 lazyeval_0.2.2 ade4_1.7-16 tidyselect_1.1.0
[13] prettyunits_1.1.1 bit_4.0.4 curl_4.3 compiler_3.6.3
[17] graph_1.64.0 formatR_1.7 RBGL_1.62.1 askpass_1.1
[21] rappdirs_0.3.3 stringr_1.4.0 pkgconfig_2.0.3 dbplyr_2.1.0
[25] fastmap_1.1.0 ensembldb_2.10.2 limma_3.42.2 BSgenome_1.54.0
[29] regioneR_1.18.1 rlang_0.4.10 rstudioapi_0.13 RSQLite_2.2.3
[33] generics_0.1.0 dplyr_1.0.4 RCurl_1.98-1.2 magrittr_2.0.1
[37] GO.db_3.10.0 GenomeInfoDbData_1.2.2 Matrix_1.2-18 Rcpp_1.0.6
[41] fansi_0.4.2 lifecycle_1.0.0 stringi_1.5.3 MASS_7.3-51.5
[45] zlibbioc_1.32.0 BiocFileCache_1.10.2 blob_1.2.1 crayon_1.4.1
[49] lattice_0.20-38 splines_3.6.3 multtest_2.42.0 GenomicFeatures_1.38.2
[53] hms_1.0.0 pillar_1.5.0 seqinr_4.2-5 futile.options_1.0.1
[57] XML_3.99-0.3 glue_1.4.2 lambda.r_1.2.4 BiocManager_1.30.10
[61] idr_1.2 vctrs_0.3.6 openssl_1.4.3 purrr_0.3.4
[65] assertthat_0.2.1 cachem_1.0.4 AnnotationFilter_1.10.0 survival_3.1-8
[69] tibble_3.1.0 AnnotationDbi_1.48.0 ellipsis_0.3.1