GC_content_over_grl: Retrieve GC content level from genome over regions defined by...
In exomePeak2: Bias Awared Peak Calling and Quantification for MeRIP-Seq

The GC content is calculated only on exon sequences, for regions that failed to mapped to exons in txdb, the function would return NA instead. The ranges in grl will be flanked by the size fragment_length - binding_length before GC content calculation.

GC_content_over_grl(
  bsgenome,
  txdb,
  grl,
  fragment_length = 100,
  binding_length = 25,
  effective_GC = FALSE
)

`bsgenome`	A BSgenome object.
`txdb`	A TxDb object.
`grl`	A GRangesList object.
`fragment_length`	A positive integer of the expected fragment length in the RNA-Seq library; Default 100.
`binding_length`	A positive integer of the expected antibody binding length of IP; Default 25.
`effective_GC`	If TRUE, the GC content calculation will be weighted by the fragment mapping probabilities, currently it is only supported for the single based modification annotation; Default FALSE.

a DataFrame contains 2 columns:

1. GC_content: the (effective) GC content of each GRanges / GRangesList element 2. Indx_length: the calculated total feature length used to quantify reads.

exomePeak2 documentation built on Nov. 8, 2020, 5:27 p.m.