reportGenes: Report Expression Information for a given set of genes

In axm323/dataVisEasy: datavisEasy: Data visualizations Using Annotations Made Easy

Report Expression Information for a given set of genes

Description

Based on supplied expression data set, will return a report detailing expression information for the list of genes supplied to the function. Will report the percent of samples with detectable expression (non-missing data), Percent Samples NA (missing data), and percent of samples high, mid-range, and low expression with respect to the median of each gene to detail the range of expression of the genes in question.

Usage

reportGenes(data, list,exact = T, ranges = "fixed", fixed.range = 2, weight = 1.25)

Arguments

data	numeric data matrix with samples/observations in the columns and genes/variables in the rows
list	character vector of genes/variables to be pulled out of the data matrix for report of expression ranges
exact	whether or not to search for exact or inexact matches of 'list' in 'data'. If exact = T (default) heatmap will plot genes/variables that exactly match the list supplied. If set to FALSE, will search for inexact matches.
ranges	option dictating how the range the ranges of expression are determined. The default, "fixed" sets the threshold for high and low expression a fixed value away from the median. Will also accept "mad" which sets these thresholds as a function of the median average deviation from the median.
fixed.range	if ranges = "fixed". Indicates the threshold away from the median where expression is considered high or low. For the default case where fixed.range = 2, expression > median() + 2 will be considered high expression while expression < median() - 2 will be considered low expression with all values in between considered mid range.
weight	if ranges = "mad". Indicates the weight applied to the mad that sets the threshold away from the median where expression is considered high or low. For the default case where weight = 1.25, expression > median() + mad*1.25 will be considered high expression while expression < median() - mad*1.25 will be considered low expression with all values in between considered mid range.

Value

a data frame with six columns: Gene, Percent Samples Detected, Percent Samples NA, Percent High Expressing, Percent Mid-Range Expression, and Percent Low Expressing

Author(s)

~~Alison Moss~~

Examples

##assess percentage of samples detected and distribution of expression for select genes
reportGenes(RAGP_norm, list = c("Th","Chat","Npy","PGP9.5","NeuN"))

##fixed range above/below median
reportGenes(RAGP_norm, list = c("Th","Chat","Npy","PGP9.5","NeuN"),
  ranges = "fixed", fixed.range = 1)

##based on fraction (weight) of median average deviation (mad) from median
reportGenes(RAGP_norm, list = c("Th","Chat","Npy","PGP9.5","NeuN"),
  ranges = "mad", weight = 0.5)
reportGenes(RAGP_norm, list = c("Th","Chat","Npy","PGP9.5","NeuN"),
  ranges = "mad", weight = 1)

axm323/dataVisEasy documentation built on Feb. 1, 2024, 11:53 p.m.