plgem.write.summary {plgem}R Documentation

Write a list of differentially expressed genes/proteins to the disk

Description

This function writes the list of differentially expressed genes/proteins obtained via a call to either plgem.deg or run.plgem to a series of files in the current working directory.

Usage

  plgem.write.summary(x, verbose=FALSE)

Arguments

x list; the output of either plgem.deg or run.plgem, i.e. a list of list(s) of named vectors.
verbose logical; if TRUE, comments are printed out while running.

Details

The gene or protein lists are written to the current working directory, using conveniently chosen filenames that reflect the specific comparisons that were performed (i.e. which experimental condition was compared to the baseline) and the specific significance threshold that were used in the DEG selection step.

Value

The function returns no value. It is called for its side effect to write files to the working directory.

Author(s)

Mattia Pelizzola mattia.pelizzola@gmail.com Norman Pavelka nxp@stowers-institute.org

References

Pavelka N, Pelizzola M, Vizzardelli C, Capozzoli M, Splendiani A, Granucci F, Ricciardi-Castagnoli P. A power law global error model for the identification of differentially expressed genes in microarray data. BMC Bioinformatics. 2004 Dec 17;5:203.; http://www.biomedcentral.com/1471-2105/5/203

Pavelka N, Fournier ML, Swanson SK, Pelizzola M, Ricciardi-Castagnoli P, Florens L, Washburn MP. Statistical similarities between transcriptomics and quantitative shotgun proteomics data. Mol Cell Proteomics. 2007 Nov 19; http://www.mcponline.org/cgi/content/abstract/M700240-MCP200v1

See Also

plgem.deg, run.plgem

Examples

  ## Not run:
  data(LPSeset)
  LPSdegList <- run.plgem(LPSeset)
  plgem.write.summary(LPSdegList, verbose=TRUE)
  ## End(Not run)

[Package plgem version 1.14.0 Index]