Description Usage Arguments Value Author(s) Examples
For splice variants, obtain counts of compatible fragments spanning
the start and/or end of each variant.
Counts can be obtained from an SGFeatureCounts
object
or from BAM files. Only one of the two arguments feature_counts
or sample_info
must be specified. Local estimates of relative
usage are calculated at the start and/or end of each splice variant.
For splice variants with relative usage estimates at both start and end,
these are combined by taking a weighted mean, where weights are
proportional to the total number of reads spanning the respective
boundary.
1 2 | getSGVariantCounts(variants, feature_counts = NULL, sample_info = NULL,
min_denominator = NA, min_anchor = 1, verbose = FALSE, cores = 1)
|
variants |
|
feature_counts |
|
sample_info |
Data frame with sample information.
Required columns are “sample_name”, “file_bam”,
“paired_end”, “read_length”, “frag_length”
and “lib_size”. Library information can be obtained with
function |
min_denominator |
Integer specifying minimum denominator when
calculating variant frequencies. The total number of boundary-spanning
reads must be equal to or greater than |
min_anchor |
Integer specifiying minimum anchor length |
verbose |
If |
cores |
Number of cores available for parallel processing |
SGVariantCounts
object
Leonard Goldstein
1 2 3 4 | sgvc_from_sgfc <- getSGVariantCounts(sgv_pred, sgfc_pred)
path <- system.file("extdata", package = "SGSeq")
si$file_bam <- file.path(path, "bams", si$file_bam)
sgvc_from_bam <- getSGVariantCounts(sgv_pred, sample_info = si)
|
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