siscreenr-package: siscreenr: High Throughput Data Analysis
In olobiolo/siscreenr: Analyze Genome-Wide siRNA Screening Campaigns

Description Details Functions Author(s) See Also

A package for analyzing high throughput microscopy data produced by Olympus ScanR systems. Provides tools for loading, normalizing and scoring data, and hit selection. It is intended for interactive use so most of the functions leave a considerable amount of work to the user.

The data is obtained with an automated fluorescence microscope and preliminary image analysis is done with ScanR software. Most experiments are done in 384 well plate format and usually involve dozens of plates. However, it is compatible with other plate formats and some concepts can be transferred to slides as well.

Data analysis:

build_screen collate all data into a single data frame, rearrange and add layout
mask_values set selected values to NA so that they are omitted from the analysis
normalize normalize data by one of the available methods: subtract mean/median of reference or Tukey's median polish (for matrices)
zscore calculate (robust) z scores
hitscore classify data point as hit or not based on a given threshold; usually used on z scores
flag_hits calculate aggregate hit score and assign hit status to data points

Data formatting:

clean_column_names clean up superfluous characters from column names
insert_zeros inset zeros to elements of a character vector (e.g. well positions)
separate_flag change character note on a plate into a logical flag on single wells

File preparation:

fetch_files copy all result files from a screen directory to one location
layouts prepare layout file from components
update_annotation update library annotation
patch_annotation fix errors in library annotation left by update_annotation

Visualization:

plot_screen_progress create a plot of material accumulation/processing over time
drawmeabarplot plot mean green fraction z scores and highlight desired genes
color_sections prepare plotting space for highlight_genes
highlight_genes draw scatterplot of entire screen and highlight desired genes

Miscellaneous:

attach_annotation add annotation to screen object
plate.type.converter internal function that translates plate type codes
show_conversion_key print the key for plate type conversion by plate.type.converter
edit_conversion_key edit the key for plate type conversion
recover_conversion_key restore the original key for plate type conversion
scan_status report on the status of the latest and any acquisition errors
retry rerun call that randomly fails; taken from package acutils