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. |