ballgownrsem {ballgown} | R Documentation |
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 |
gtf |
path to GTF file of genes/transcripts used in your RSEM reference.
(where the reference location was denoted by the |
UCSC |
set to TRUE if |
tfield |
What keyword identifies transcripts in the "attributes" field
of |
attrsep |
How are attributes separated in the "attributes" field of
|
bamout |
set to |
pData |
data frame of phenotype data, with rows corresponding to
|
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