## ----echo = FALSE------------------------------------------------------------- library(knitr) opts_chunk$set( error = FALSE, tidy = FALSE, message = FALSE, warning = FALSE, fig.align = "center" ) ## ----Package installation, echo= TRUE, eval=FALSE----------------------------- # #Installation from Github: # devtools::install_github("Drinchai/BloodGen3Module") # # #Installation from Bioconductor: # if (!requireNamespace("BiocManager", quietly=TRUE)) # install.packages("BiocManager") # BiocManager::install("BloodGen3Module") # ## ----setup, warning=FALSE,message=FALSE, echo= TRUE--------------------------- library(BloodGen3Module) ## ----raw data and annotaion preparation, warning=FALSE,message=FALSE,echo= TRUE---- #Load expression data #Example expression data for package testting library(ExperimentHub) library(SummarizedExperiment) dat = ExperimentHub() res = query(dat , "GSE13015") GSE13015 = res[["EH5429"]] ## ----group comparison analysis using t-test statistical analysis, warning=FALSE, echo= TRUE---- Group_df <- Groupcomparison(GSE13015, sample_info = NULL, FC = 1.5, pval = 0.1 , FDR = TRUE, Group_column = "Group_test", Test_group = "Sepsis", Ref_group = "Control", SummarizedExperiment = TRUE) ## ----group comparison analysis using limma statistical analysis,warning=FALSE---- Group_limma <- Groupcomparisonlimma(GSE13015, sample_info = NULL, FC = 1.5, pval = 0.1 , FDR = TRUE, Group_column = "Group_test", Test_group = "Sepsis", Ref_group = "Control", SummarizedExperiment = TRUE) ## ----grid visulization after running group comparison analysis---------------- gridplot(Group_df, cutoff = 15, Ref_group = "Control", filename= tempfile()) ## ----individual single sample analysis, warning=FALSE, echo= TRUE------------- Individual_df = Individualcomparison(GSE13015, sample_info = NULL, FC = 1.5, DIFF = 10, Group_column = "Group_test", Ref_group = "Control", SummarizedExperiment = TRUE) ## ----fingerprint visualization, warning=FALSE--------------------------------- fingerprintplot(Individual_df, sample_info = NULL, cutoff = 15, rowSplit= TRUE , Group_column= "Group_test", show_ref_group = FALSE, Ref_group = "Control", Aggregate = "A28", filename = tempfile() , height = NULL, width = NULL)