ballgown-class: Ballgown

In alyssafrazee/ballgown: Flexible, isoform-level differential expression analysis

Description

S4 class for storing and manipulating expression data from assembled transcriptomes

Slots

expr

tables containing expression data for genomic features (introns, exons, transcripts)

structure

genomic locations of features and their relationships to one another

indexes

tables connecting components of the assembly and providing other experimental information (e.g., phenotype data and locations of read alignment files)

dirs

directories holding data created by tablemaker

mergedDate

date the ballgown object was created

meas

which expression measurement(s) the object contains in its data slot. Vector of one or more of "rcount", "ucount", "mrcount", "cov", "cov_sd", "mcov", "mcov_sd", or "FPKM", if Tablemaker output is used, or one of "TPM" or "FPKM" if RSEM output is used. Can also be "all" for all measurements. See vignette for details.

RSEM

TRUE if object was made from RSEM output, FALSE if object was made from Tablemaker/Cufflinks output.

Author(s)

Alyssa Frazee, Leonardo Collado-Torres, Jeff Leek

Examples

  data(bg)
  class(bg) #"ballgown"
  dim(bg@expr$exon)
  bg@structure$exon
  head(bg@indexes$t2g)
  head(bg@dirs)
  bg@mergedDate
  bg@meas
  bg@RSEM

alyssafrazee/ballgown documentation built on Sept. 3, 2021, 7:15 p.m.