## ----include = TRUE, echo = FALSE, message = FALSE, warning = FALSE----------- library(OMICsPCAdata) library(kableExtra) library(rmarkdown) library(knitr) library(MultiAssayExperiment) ## ----setup, include = FALSE--------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#", eval = TRUE ) ## ----global_options, include=FALSE-------------------------------------------- knitr::opts_chunk$set(fig.pos = 'H') ## ----echo = FALSE------------------------------------------------------------- datalist <- data(package = "OMICsPCAdata") datanames <- datalist$results[,3] data(list = datanames) assays <- assays(multi_assay) ## ----echo =FALSE-------------------------------------------------------------- data_summary = data.frame( Name = c( "CAGE" ,"H2az" ,"H3k9ac", "H3k4me1"), Type_of_Assay = c( "Expression of Transcription Start Sites(TSS)", "location of Histone modification peaks", "location of Histone modification peaks", "location of Histone modification peaks" ), No_of_Cell_lines =c( ncol(assays$CAGE), ncol(assays$H2az), ncol(assays$H3k9ac), ncol(assays$H3k4me1) ), Name_of_Cell_lines = c( paste(names(assays$CAGE), collapse = " ,"), paste(names(assays$H2az), collapse = " ,"), paste(names(assays$H3k9ac), collapse = " ,"), paste(names(assays$H3k4me1), collapse = " ,") ), Type_of_data = c( "Cap Analysis\nof\nGene Expression", "ChIP-seq", "ChIP-seq", "ChIP-seq" ) ) names(data_summary) <- c("Assay", "Assay\nType", "Number of\nCell lines", "Name of\ncell lines", "Experiment") ## ----eval = TRUE, echo=FALSE, results='asis'---------------------------------- #for html knitr::kable(data_summary, caption = "Summary of data sets", align = 'c') %>% kable_styling("bordered",full_width = FALSE, position = "center") %>% column_spec(1, bold = FALSE, border_right = FALSE, border_left = FALSE, width = "5em") %>% column_spec(2, bold = FALSE, border_right = FALSE, border_left = FALSE, width = "5em") %>% column_spec(3, border_right = FALSE, width = "4em") %>% column_spec(4, border_right = FALSE, width = "23em") %>% column_spec(5, border_right = FALSE, width = "5em") ## ----------------------------------------------------------------------------- # The CAGE data set contains normalized CAGE data of 28770 GENCODE #TSS groups in from 31 cell lines dim(assays$CAGE) # Let's look at the first five rows and columns of this dataset head(assays$CAGE[1:5,1:5])