ballgownrsem: load RSEM data into a ballgown object
In alyssafrazee/ballgown: Flexible, isoform-level differential expression analysis

Description Usage Arguments Details Value See Also Examples

Loads results of rsem-calculate-expression into a ballgown object for easy visualization, processing, and statistical testing

ballgownrsem(
  dir = "",
  samples,
  gtf,
  UCSC = TRUE,
  tfield = "transcript_id",
  attrsep = "; ",
  bamout = "transcript",
  pData = NULL,
  verbose = TRUE,
  meas = "all",
  zipped = FALSE
)

`dir`	output directory containing RSEM output for all samples (i.e. for each run of rsem-calculate-expression)
`samples`	vector of sample names (i.e., of the `sample_name` arguments used in each RSEM run)
`gtf`	path to GTF file of genes/transcripts used in your RSEM reference. (where the reference location was denoted by the `reference_name` argument used in rsem-calculate-expression). RSEM references can be created with or without a GTF file, but currently the ballgown reader requires the GTF file.
`UCSC`	set to TRUE if `gtf` comes from UCSC: quotes will be stripped from transcript identifiers if so.
`tfield`	What keyword identifies transcripts in the "attributes" field of `gtf`? Default `'transcript_id'`.
`attrsep`	How are attributes separated in the "attributes" field of `gtf`? Default `'; '` (semicolon-space).
`bamout`	set to `'genome'` if `--output-genome-bam` was used when running rsem-calculate-expression; set to `'none'` if `--no-bam-output` was used when running rsem-calculate-expression; otherwise use the default (`'transcript'`).
`pData`	data frame of phenotype data, with rows corresponding to `samples`. The first column of `pData` must be equal to `samples`, and rows must be in the same order as `samples`.
`verbose`	If TRUE (as by default), status messages are printed during data loading.
`meas`	character vector containing either "all" or one of "FPKM" or "TPM". The resulting ballgown object will only contain the specified expression measurement for the transcripts. "all" creates the full object.
`zipped`	set to TRUE if all RSEM results files have been gzipped (end) in ".gz").

Currently exon- and intron-level measurements are not available for RSEM-generated ballgown objects, but development is ongoing.

a ballgown object with the specified expression measurements and structure specified by GTF.

ballgown for reading Cufflinks/Tablemaker output

dataDir = system.file('extdata', package='ballgown')
gtf = file.path(dataDir, 'hg19_genes_small.gtf.gz')
rsemobj = ballgownrsem(dir=dataDir, samples=c('tiny', 'tiny2'), gtf=gtf,
    bamout='none', zipped=TRUE)
rsemobj