## ----setup, include=FALSE----------------------------------------------------- knitr::opts_chunk$set(fig.width = 7, fig.height = 7, echo = FALSE, warning = FALSE, message = FALSE, dev = 'png', out.extra = 'style="border-width: 0;"') ## ----echo = TRUE-------------------------------------------------------------- rep1_df <- idr2d:::chipseq$rep1_df rep2_df <- idr2d:::chipseq$rep2_df ## ----------------------------------------------------------------------------- library(DT) header <- htmltools::withTags(table( class = 'display', thead( tr( th("chromosome"), th("start coordinate"), th("end coordinate"), th("score") ) ) )) datatable(rep1_df[seq_len(min(nrow(rep1_df), 1000)), ], container = header, rownames = FALSE, options = list(searching = FALSE)) %>% formatRound("value", 3) ## ----------------------------------------------------------------------------- datatable(rep2_df[seq_len(min(nrow(rep2_df), 1000)), ], container = header, rownames = FALSE, options = list(searching = FALSE)) %>% formatRound("value", 3) ## ----echo = TRUE-------------------------------------------------------------- library(idr2d) ## ----echo = TRUE-------------------------------------------------------------- idr_results <- estimate_idr1d(rep1_df, rep2_df, value_transformation = "log") rep1_idr_df <- idr_results$rep1_df ## ----------------------------------------------------------------------------- chr <- start <- end <- rank <- rep_rank <- value <- rep_value <- idr <- NULL header <- htmltools::withTags(table( class = 'display', thead( tr( th("chr."), th("start coordinate"), th("end coordinate"), th("rank in R1"), th("rank in R2"), th("transformed value in R1"), th("transformed value in R2"), th("IDR") ) ) )) df <- dplyr::select(rep1_idr_df, chr, start, end, rank, rep_rank, value, rep_value, idr) datatable(df[seq_len(min(nrow(df), 1000)), ], rownames = FALSE, options = list(searching = FALSE), container = header) %>% formatRound(c("value", "rep_value", "idr"), 3) ## ----echo = TRUE-------------------------------------------------------------- summary(idr_results) ## ----echo = TRUE-------------------------------------------------------------- draw_idr_distribution_histogram(rep1_idr_df) ## ----echo = TRUE-------------------------------------------------------------- draw_rank_idr_scatterplot(rep1_idr_df) ## ----echo = TRUE-------------------------------------------------------------- draw_value_idr_scatterplot(rep1_idr_df)