Cpg#
Set of discriminant functions that can recognize structural and compositional features
API#
Set of discriminant functions that can recognize structural and compositional features such as CpG islands, promoter regions and first splice-donor sites. .. rubric:: References
[4]
- ensembl.tools.anno.simple_feature_annotation.cpg.run_cpg(genome_file, output_dir, cpg_bin=PosixPath('cpg_lh'), cpg_min_length=400, cpg_min_gc_content=50, cpg_min_oe=0.6, num_threads=1, bedtools_bin='/hps/software/users/ensembl/ensw/C8-MAR21-sandybridge/linuxbrew/bin/bedtools')[source]#
Run CpG islands on genomic slices
- param genome_file:
Genome file path.
- type genome_file:
PathLike
- param output_dir:
Working directory path
- type output_dir:
Path
- param cpg_bin:
CpG software path.
- type cpg_bin:
Path
- param cpg_min_length:
Min length of CpG islands
- type cpg_min_length:
int
- param cpg_min_gc_content:
Min GC frequency percentage
- type cpg_min_gc_content:
int
- param cpg_min_oe:
Min ratio of the observed to expected number of CpG (CpGo/e)
- type cpg_min_oe:
float
- param num_threads:
int, number of threads.
- type num_threads:
int
- param bedtools_bin:
Bedtools executable path.
- type bedtools_bin:
str
- return:
None
- rtype:
None