ballgownrsem {ballgown} | R Documentation

## load RSEM data into a ballgown object

### Description

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

### Usage

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

### Arguments

`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").

### Details

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

### Value

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

### See Also

`ballgown` for reading Cufflinks/Tablemaker output

### Examples

    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

[Package ballgown version 2.20.0 Index]