ballgown-class {ballgown} | R Documentation

## Ballgown

### 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

[Package ballgown version 2.19.3 Index]