calc_mean_sd_background: Calculate the mean and the standard deviation.

In flowQB: Automated Quadratic Characterization of Flow Cytometer Instrument Sensitivity: Q, B and CV instrinsic calculations

Description

This method looks at all channels except those specified in the ignore_channel list and calculated the mean and the standard deviation for those channels.

Usage

    calc_mean_sd_background(fcs_file_path, ignore_channels)

Arguments

fcs_file_path	A character string specifying the file path to the FCS file with the acquired bead data.
ignore_channels	A vector of short channel names (values of the $PnN keywords) specifying channels that should not be considered for the fitting procedure. Normally, those should be all non-fluorescence channels, such as the time and the (forward and side) scatter channels.

Details

The getOutliers method from the extremevalues package is used to calculate the mean and the standard deviation values for all the FCS channels in the file except those specified in the ignore channels list.

Value

The result is a data frame with columns corresponding to short channel names of channels from the input FCS file except those specified by the ignore_channels parameter. The rows include the total number of events, the mean and the standard deviation.

Author(s)

Josef Spidlen, Wayne Moore, Faysal El Khettabi

See Also

calc_mean_sd_197, calc_mean_sd_duke, calc_mean_sd_capture, calc_mean_sd_capture_all

Examples

    library(flowCore)
    library(xlsx)
    library(flowQBData)

    inst_xlsx_path <- system.file("extdata", 
        "140126_InstEval_Stanford_LSRIIA2.xlsx", package="flowQBData")
    xlsx <- read.xlsx(inst_xlsx_path, 1, headers=FALSE, stringsAsFactors=FALSE)
    
    ignore_channels_row <- 9
    ignore_channels <- vector()
    i <- 1
    while(!is.na(xlsx[[i+4]][[ignore_channels_row]])) {
        ignore_channels[[i]] <- xlsx[[i+4]][[ignore_channels_row]]
        i <- i + 1
    }
    
    instrument_folder_row <- 9
    instrument_folder_col <- 2
    instrument_folder <- xlsx[[instrument_folder_col]][[instrument_folder_row]]

    test_column <- 15
    test_row <- 14
    folder <- xlsx[[test_column]][[test_row]]
    file_name <- xlsx[[test_column]][[test_row+1]]

    fcs_path <- system.file("extdata",
        instrument_folder, folder, file_name, package="flowQBData")

    results <- calc_mean_sd_background(fcs_path, ignore_channels)

    ## Same thing as above with providing the arguments directly without
    ## parsing it from the spreadsheet.
    fcs_path <- system.file("extdata", "SSFF_LSRII", "Other_Tests", 
        "935319.fcs", package="flowQBData")
    ignore_channels <- c(
        "Time", "FSC-A", "FSC-W", "FSC-H", "SSC-A", "SSC-W", "SSC-H")
    results <- calc_mean_sd_background(fcs_path, ignore_channels)

flowQB documentation built on May 6, 2019, 3:05 a.m.