subset {ballgown} | R Documentation |
subset ballgown objects to specific samples or genomic locations
subset(x, ...) ## S4 method for signature 'ballgown' subset(x, cond, genomesubset = TRUE)
x |
a ballgown object |
... |
further arguments to generic subset |
cond |
Condition on which to subset. See details. |
genomesubset |
if TRUE, subset |
To use subset
, you must provide the cond
argument as a
string representing a logical expression specifying your desired subset.
The subset expression can either involve column names of
texpr(x, "all")
(if genomesubset
is TRUE
) or of
pData(x)
(if genomesubset
is FALSE
). For example, if
you wanted a ballgown object for only chromosome 22, you might call
subset(x, "chr == 'chr22'")
. (Be sure to handle quotes within
character strings appropriately).
a subsetted ballgown object, containing only the regions or samples
satisfying cond
.
Alyssa Frazee
data(bg) bg_twogenes = subset(bg, "gene_id=='XLOC_000454' | gene_id=='XLOC_000024'") bg_twogenes # ballgown instance with 4 assembled transcripts and 20 samples bg_group0 = subset(bg, "group == 0", genomesubset=FALSE) bg_group0 # ballgown instance with 100 assembled transcripts and 10 samples