## ----setup, include=FALSE----------------------------------------------------- knitr::opts_chunk$set(echo=TRUE) knitr::opts_knit$set(progress=FALSE, verbose=FALSE) ## ----echo=FALSE, out.width='70%', fig.align='center'-------------------------- knitr::include_graphics('db_structure.png') ## ----echo=FALSE, fig.align='left'--------------------------------------------- knitr::include_graphics('input_contents_table.PNG') ## ----results='hide', message=FALSE-------------------------------------------- library(RIPAT) # Download gene data file makeData(organism = 'GRCh37', dataType = 'gene') ## ----results='hide', message=FALSE-------------------------------------------- blast_obj=makeInputObj(inFile='blast_result.txt', vectorPos='front', mapTool='blast', outPath='.', outFileName='A5_15856M_BLAST') ## ----results='hide', message=FALSE-------------------------------------------- blast_gene10K=annoByGene(hits=blast_obj, organism='GRCh37', interval=5000, range=c(-20000, 20000), doRandom=TRUE, randomSize=10000, includeUndecided=FALSE, outPath='.', outFileName='A5_15856M_BLAST_10K') ## ----echo=FALSE--------------------------------------------------------------- knitr::include_graphics('A5_15856M_BLAST_10K_distribution_gene_GRCh37.png') ## ----echo=FALSE--------------------------------------------------------------- knitr::include_graphics('A5_15856M_BLAST_10K_distribution_tss_GRCh37.png') ## ----results='hide', message=FALSE-------------------------------------------- blast_gene_norandom=annoByGene(hits=blast_obj, organism='GRCh37', interval=5000, range=c(-20000, 20000), doRandom=FALSE, includeUndecided=FALSE, outPath='.', outFileName='A5_15856M_BLAST_norandom') ## ----echo=FALSE--------------------------------------------------------------- knitr::include_graphics('A5_15856M_BLAST_norandom_distribution_gene_GRCh37.png') ## ----echo=FALSE--------------------------------------------------------------- knitr::include_graphics('A5_15856M_BLAST_norandom_distribution_tss_GRCh37.png') ## ----results='hide', message=FALSE-------------------------------------------- ## Karyogram marked genomic spots karyo_obj_gene = drawingKaryo(hits=blast_obj, organism="GRCh37", feature=blast_gene10K$Gene_data, includeUndecided=FALSE, outPath=getwd(), outFileName='A5_15856M_BLAST_karyo_gene') ## ----echo=FALSE--------------------------------------------------------------- knitr::include_graphics('Ideogram_A5_15856M_BLAST_karyo_gene_GRCh37_decided.png') ## ----results='hide', message=FALSE-------------------------------------------- makeDocument(res = blast_gene10K, dataType = 'gene', excelOut = TRUE, includeUndecided = FALSE, outPath = getwd(), outFileName = 'A5_15856M_BLAST_10K') ## ----echo=FALSE--------------------------------------------------------------- knitr::include_graphics('A5_15856M_BLAST_10K_histogram_observed_gene.png') ## ----echo=FALSE--------------------------------------------------------------- knitr::include_graphics('A5_15856M_BLAST_10K_random_histogram_observed_gene.png') ## ----echo=FALSE--------------------------------------------------------------- knitr::include_graphics('A5_15856M_BLAST_10K_pvalue_plot_gene.png') ## ----echo=FALSE--------------------------------------------------------------- citation('RIPAT')