Skip to content

Latest commit

 

History

History
39 lines (32 loc) · 2.33 KB

README.md

File metadata and controls

39 lines (32 loc) · 2.33 KB
Raw

DGEobj.utils: A toolkit facilitating a limma/voom workflow Differential Gene Expression analysis

CRAN_Status_Badge CRAN_Downloads_Badge CircleCI build status Codecov test coverage

This package implements a set of utility functions to enable a limma/voom workflow capturing the results in the DGEobj data structure. Aside from implementing a well developed and popular workflow in DGEobj format, the run* functions in the package illustrate how to wrap the individual processing steps in a workflow in functions that capture important metadata, processing parameters, and intermediate data items in the DGEobj data structure. This function- based approach to utilizing the DGEobj data structure insures consistency among a collection of projects processed by these methods and thus facilitates downstream automated meta-analysis.

Functionality includes:

Analysis

  • runContrasts: Build contrast matrix and calculate contrast fits
  • runEdgeRNorm: Run edgeR normalization on DGEobj
  • runIHW: Apply Independent Hypothesis Weighting (IHW) to a list of topTable dataframes
  • runPower: Run a power analysis on counts and design matrix
  • runQvalue: Calculate and add q-value and lFDR to dataframe
  • runSVA: Test for surrogate variables
  • runVoom: Run functions in a typical voom/lmFit workflow

Utilities

  • convertCounts: Convert count matrix to CPM, FPKM, FPK, or TPM
  • extractCol: Extract a named column from a series of df or matrices
  • lowIntFilter: Apply low intensity filters to a DGEobj
  • rsqCalc: Calculate R-squared for each gene fit
  • summarizeSigCounts: Summarize a contrast list
  • topTable.merge: Merge specified topTable df cols
  • tpm.direct: Convert countsMatrix and geneLength to TPM units
  • tpm.on.subset: Calculate TPM for a subsetted DGEobj