plateStatistics: Bias inspection per plate

In uzh/ezRun: An R meta-package for the analysis of Next Generation Sequencing Data

Bias inspection per plate

Description

Calculate counts/concentration in a plate layout and plot in heatmaps.

Usage

  plateStatistics(dataset, colname = c("Read Count",
                                       "LibConc_qPCR [Characteristic]",
                                       "LibConc_100_800bp [Characteristic]"))
  heatmapPlate(x, title="unnamed", center=TRUE, log10=TRUE)                                       

Arguments

dataset	A data.frame read from “input_dataset.tsv”.
title	A character(1): title of the plate heatmap.
x	A matrix of counts/concentration of a plate.
center	A boolean. When TRUE, plot the heatmaps value from half of median to twice of median.
log10	A boolean. When TRUE, plot the log10 value.

Details

plateStatistics fetch the plate position information from the column “PlatePosition [Characteristic]”. The current supported format of “PlatePosition [Characteristic]” is “PlateNumber_[A-Z][Integer]”, e.g. “1_A2”.

heatmapPlate plot the heatmap with the results from plateStatistics.

Value

plateStatistics: a list of list of matrix with rows in alphabets and columns in numbers of the plate.

heatmapPlate: plotly object of heatmap.

Author(s)

Ge Tan

References

Plate layout: https://www.dnaseq.co.uk/images/samples-on-well-plate.png

Examples

  ## Not run: 
    dataset <- ezRead.table("/srv/gstore/projects/p2438/Fastqc_18564_2017-06-07--14-06-33/input_dataset.tsv")
    ans <- plateStatistics(dataset)
    
    p1 <- heatmapPlate(ans[[1]][["Read Count"]], center=TRUE, log10=TRUE)
    p2 <- heatmapPlate(ans[[1]][["Read Count"]], center=TRUE, log10=FALSE)
    p3 <- heatmapPlate(ans[[1]][["Read Count"]], center=FALSE, log10=TRUE)
    p4 <- heatmapPlate(ans[[1]][["Read Count"]], center=FALSE, log10=FALSE)
    subplot(p1, p3,p2,p4, nrows=2)
  
## End(Not run)

uzh/ezRun documentation built on Dec. 26, 2024, 9:53 a.m.