## ----include = FALSE---------------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>", warning = FALSE ) ## ----'install', eval = FALSE-------------------------------------------------- # if (!requireNamespace("BiocManager", quietly = TRUE)) { # install.packages("BiocManager") # } # # BiocManager::install("scifer") ## ----setup-------------------------------------------------------------------- library(ggplot2) library(scifer) ## ----check_fcs, message=FALSE------------------------------------------------- fcs_data <- fcs_processing( folder_path = system.file("/extdata/fcs_index_sorting",package = "scifer"), compensation = FALSE, plate_wells = 96, probe1 = "FSC.A", probe2 = "SSC.A", posvalue_probe1 = 600, posvalue_probe2 = 400) fcs_plot(fcs_data) ## ----channels----------------------------------------------------------------- colnames(fcs_data) ## ----check_fcs_noprobe, message=FALSE, warning=FALSE-------------------------- fcs_data <- fcs_processing( folder_path = system.file("/extdata/fcs_index_sorting",package = "scifer"), compensation = FALSE, plate_wells = 96, probe1 = "FSC.A", probe2 = "SSC.A", posvalue_probe1 = 0, posvalue_probe2 = 0) fcs_plot(fcs_data) ## ----check_fcs_probe, message=FALSE, warning=FALSE---------------------------- fcs_data <- fcs_processing( folder_path = system.file("/extdata/fcs_index_sorting",package = "scifer"), compensation = FALSE, plate_wells = 96, probe1 = "Pre.F", probe2 = "Post.F", posvalue_probe1 = 600, posvalue_probe2 = 400) fcs_plot(fcs_data) ## ----check_fcs_probe_compensated, message=FALSE, warning=FALSE---------------- fcs_data <- fcs_processing( folder_path = system.file("/extdata/fcs_index_sorting",package = "scifer"), compensation = TRUE, plate_wells = 96, probe1 = "Pre.F", probe2 = "Post.F", posvalue_probe1 = 600, posvalue_probe2 = 400) fcs_plot(fcs_data) ## ----specificity, message=FALSE, warning=FALSE-------------------------------- unique(fcs_data$specificity) ## ----bcr_sequence, warning=FALSE---------------------------------------------- ## Read abif using sangerseqR package abi_seq <- sangerseqR::read.abif( system.file("/extdata/sorted_sangerseq/E18_C1/A1_3_IgG_Inner.ab1", package="scifer")) ## Summarise using summarise_abi_file() summarised <- summarise_abi_file(abi_seq) head(summarised[["summary"]]) head(summarised[["quality_score"]]) ## ----bcr_sequences, warning=FALSE--------------------------------------------- sf <- summarise_quality( folder_sequences=system.file("extdata/sorted_sangerseq", package="scifer"), secondary.peak.ratio=0.33, trim.cutoff=0.01, processor = 1) ## ----bcr_seq_columns, warning=FALSE------------------------------------------- ## Print names of all the variables colnames(sf[["summaries"]]) ## ----bcr_seq_table, warning=FALSE--------------------------------------------- ## Print table head(sf[["summaries"]][4:10]) ## ----eval=FALSE--------------------------------------------------------------- # quality_report( # folder_sequences = system.file("extdata/sorted_sangerseq", package="scifer"), # outputfile = "QC_report.html", output_dir = "~/full/path/to/your/location", # folder_path_fcs = system.file("extdata/fcs_index_sorting", # package = "scifer"), # probe1 = "Pre.F", probe2 = "Post.F", # posvalue_probe1 = 600, posvalue_probe2 = 400) ## ----session_info------------------------------------------------------------- sessionInfo()