In hyginn/BCB420.2019.ESA: Exploratory Systems Analysis Tools

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

# knitr knits in a new session with an empty global workspace after setting its
# working directory to ./vignettes. To make your package functions available in
# the vignette, you have to load the library. The following two lines should
# accomplish this without manual intervention:
pkgName <- trimws(gsub("^Package:", "", readLines("../DESCRIPTION")[1]))
library(pkgName, character.only = TRUE)

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About this Vignette

This function is capable of taking a defined system name and providing its specific expression profiles. This includes normalizing the epression levels provided by the function and then providing a mean expression for each experiment. It will additionally identify which conditions caused the system to be significantly up or down regulated.

Example and usage

If we want to see the responses of the PHALY to the various conditions present in the dataset, we will perform the following function

# Load the expression profiles:
myURL <- paste0("http://steipe.biochemistry.utoronto.ca/abc/assets/",
                "GEO-QN-profile-2019-03-24.rds")
myQNXP <- readRDS(url(myURL))  # loads quantile-normalized expression data

#Call created function
System_Expression("PHALY", myQNXP)