# A package to produce metagene plots

## Documentation for package ‘metagene’ version 2.31.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

avoid_gaps_update

Is is a function designed to remove values <= to 'gaps_threshold'. Nucleotides local and global positions, bins, size of regions/genes and exons will be recalculated. To use on metagene's table during RNA-seq analysis. Not made for ChIP-Seq analysis or to apply on matagene's data_frame. A similar function is implemented in produce_data_frame() with same arguments. The unique goal of this function is to allow permutation_test which match the plot created using avoid_gaps, bam_name and gaps_threshold arguments in the produce_data_frame function.

Bam_Handler | A class to manage BAM files.
bed_file_filter | Extract a list of ranges defined by the bed_file_content_gr argument from the ebgwot GRangesList. Equivalent to the exonsByOverlaps of GenomicFeatures.
exon_by_gene_with_observed_transcripts | Extract exons by genes for which data are available in quantification files
get_demo_bam_files | Get BAM filenames for demo
get_demo_design | Get a demo design object
get_demo_metagene | Get a demo metagene object
get_demo_regions | Get regions filenames for demo
get_promoters_txdb | Extract Entrez genes promoters from TxDb object.
metagene | A class to manage metagene analysis.
permutation_test | Perform a permutation test on 2 tables
plot_metagene | Produce a metagene plot
promoters_hg18 | Promoters regions of hg18 Entrez genes.
promoters_hg19 | Promoters regions of hg19 Entrez genes.
promoters_mm10 | Promoters regions of mm10 Entrez genes.
promoters_mm9 | Promoters regions of mm9 Entrez genes.
write_bed_file_filter_result | Transforms the bed_file_filter function output into a file.BED readable by metagene.