syn.smooth: Synaptic Smoothing pipeline

In genejockey33000/typGumbo: Scripts and Pipelines for RNAseq Analysis

Synaptic Smoothing pipeline

Description

A highly specialized pipeline for processing synaptic vesicle release assay results. It takes in a directory containing an excel file (.xlsx) in a very specific TPP format (Tracy's Proprietary Processing) and returns a set of processed csvs for each assay along with an excel file containing a summary of the results and some analytics. Each sheet from the input excel file should have 5 header rows from row 1 they must be 1) F0 (average starting fluorescence), 2) Fstim (average stim fluorescence), 3) Fun (max unquenched fluro), 4) FC_Fun-F0 (fold change of unquenched max relative to baseline(F0)), and 5) deltaF (increase in fluor in stimulated vs. F0). First column (under metrics labels) must be a space (extra column) for time values. The script will remove this column and if it contains data rather than time stamps then the data will be lost. The worksheets used to generate the csv's will often have extra columns at the end of the sheet. They start at row 6 (after the header metrics) and report average and error fluor across all measurements for a given time. There can be 2-4 of these or none. It doesn't matter as any column after the last value in the row 1 metrics will be removed. If this function returns a Java out of memory heap space error then try restarting R and then run the following line before loading typGumbo options(java.parameters = c("-XX:+UseConcMarkSweepGC", "-Xmx8192m"))

Usage

syn.smooth(in.dir, csv = TRUE, xlsx = TRUE, filter = TRUE)

Arguments

in.dir	directory where all input .csv files are located. i.e. in.dir = "LViN15", or in.dir = "LViN15/results". Can also enter path directly to excel file i.e. in.dir = "LViN15/LViN15.xlsx"
csv	Logical. Indicate whether you want to write .csv files to output directory
xlsx	Logical. Indicate whether you want to write .xlsx file with separate sheets for each output matrix to output directory. NOTE: this uses the xlsx::write.xlsx function which takes a lot of time and memory and should not be used for very large data sets (larger than 1000 observations)
filter	logical. indicating whether data should be filtered to exclude measurements with pctFC less than 2. Even with this filter off the data will be filtered to remove measurements with pctDeltaF greater than 0 (i.e. requires positive fluorescence change)

genejockey33000/typGumbo documentation built on July 20, 2023, 11:45 p.m.