normalize_spatial_effect: Apply spatial effect normalization for all plates

In matthieu-haudiquet/rothSGA: Rothstein Lab SGA Analysis Tools

Description

Adds spatial_effect and size_spatial_norm columns to a screenmill dataset.

Usage

normalize_spatial_effect(sm_data, of, death_thresh, prefix, ...)

Arguments

sm_data	A screenmill dataset (see screenmill::read_screenmill)
of	A column to apply the normalization to (as a string).
death_thresh	Death threshold for excluding slow growing strains from model fitting.
prefix	A prefix appended to plate_effect and plate_norm column names.
...	Additional parameters passed to stats::loess

Details

Uses stats::loess to fit a two degree polynomial surface of the form $colony ~ row + column$.

matthieu-haudiquet/rothSGA documentation built on May 14, 2019, 11:28 a.m.