powerCalc: Power Calculation from gene expression data information

In HEssRNA: Heritability-Based Estimation of Sample Size for RNA-Seq Data

Power Calculation from gene expression data information

Description

This function takes the required input information such as count data, sample data, etc. to calculate the power. It filters the input count data, performs DESeq2 analysis to calculate differentially expressed genes (DEGs), and then calculates the power of detecting these DEGs based on simulations.

Usage

powerCalc(
  countDat,
  smplDat,
  alpha = 0.05,
  thrsholdFC = 2,
  inptNoOfReplicates = 3,
  sims = 10
)

Arguments

countDat	A matrix or data frame of raw count data where rows represent genes and columns represent samples.
smplDat	A data frame of sample information, with at least a condition column that specifies the experimental condition of each sample.
alpha	The significance level (FDR threshold) used to identify differentially expressed genes. Default is 0.05.
thrsholdFC	The threshold for the absolute value of log2 fold change used to filter DEGs. Default is 2.
inptNoOfReplicates	The input number of replicates based on which the power will be calculated. Default is 3.
sims	The number of simulations to run for power calculation. Default is 10.

Details

Example files included with this package:

• exmplCountDat.csv: A toy dataset with count data.

• exmplSampleDat.csv: A sample dataset with metadata.

These files are stored in the inst/extdata directory and can be accessed using the system.file() function in R.

Value

A data frame containing the calculated power values and related parameters.

References

Bi et al. (2016) \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1186/s12859-016-0994-9")} Love et al. (2014) \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1186/s13059-014-0550-8")}

Examples

# Load example files
countDatPath <- system.file("extdata", "exmplCountDat.csv", package = "HEssRNA")
smplDatPath <- system.file("extdata", "exmplSampleDat.csv", package = "HEssRNA")

if (file.exists(countDatPath) && file.exists(smplDatPath)) {
  countDat <- read.csv(countDatPath)
  smplDat <- read.csv(smplDatPath)

  result <- powerCalc(countDat, smplDat)
  print(result$PowerResults)
} else {
  warning("Example data files not found.")
}

HEssRNA documentation built on April 3, 2025, 9:29 p.m.