Usage
filterFeatures(features, paired_end, read_length, frag_length, lib_size, min_junction_count = NULL, alpha, psi, beta, gamma)
Arguments
features
TxFeatures object with predicted features,
including elementMetadata columns “N”, “N_splicesite” and
“coverage”.
paired_end
Logical, TRUE for paired-end data,
FALSE for single-end data
read_length
Read length (required for use with alpha)
frag_length
Fragment length for paired-end data (required
for use with alpha)
lib_size
Number of aligned fragments (required for use with
alpha)
min_junction_count
Minimum fragment count required for a splice
junction to be included. If specified, argument alpha is ignored.
alpha
Minimum FPKM required for a splice junction to be
included. Internally, FPKMs are converted to counts, requiring arguments
read_length, frag_length and lib_size.
alpha is ignored if argument min_junction_count
is specified.
psi
Minimum splice frequency required for a splice junction
to be included
beta
Minimum relative coverage required for an internal exon
to be included
gamma
Minimum relative coverage required for a terminal exon
to be included