BioMaesteR Tutorial
biomaester-tutorial.RmdThis is a tutorial for the BiomaesteR package, an R package with convenience functions commonly requested in various types of genomic analysis within R. This package is specialized to provide bioinformatics infrastructure that can be used in a variety of genomic analysis.
Bundled Data Objects
In this section, we will explore and use the bundled data objects that come with the BiomaesteR package. Note that raw data and data comilation scripts are also included within this package. The documentation for bunlded objects can be found here. As for the data comilation, this script can be found here.
What Is Inlcuded?
First, let’s take a look at the data objects that are included in the BiomaesteR. The following objects are as of now included in the package:
Dataset Exploration
Now, let’s take a look at the first few rows of the gene coordinates for the GRCh37 assembly.
kable(gene_coordinates_grch37[1:5, ], "html") %>%
scroll_box(width = "100%")| chrom | start | end | width | strand | type | tag | ccds_id | ensembl_gene_id | hugo_symbol | source | score | gene_version | gene_source | gene_biotype | transcript_id | transcript_version | transcript_name | transcript_source | transcript_biotype | exon_number | exon_id | exon_version | protein_id | protein_version |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 11869 | 14412 | 2544 |
|
gene | NA | NA | ENSG00000223972 | DDX11L1 | ensembl_havana | NA | 4 | ensembl_havana | pseudogene | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| 1 | 14363 | 29806 | 15444 |
|
gene | NA | NA | ENSG00000227232 | WASH7P | ensembl_havana | NA | 4 | ensembl_havana | pseudogene | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| 1 | 29554 | 31109 | 1556 |
|
gene | NA | NA | ENSG00000243485 | MIR1302-10 | ensembl_havana | NA | 2 | ensembl_havana | lincRNA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| 1 | 34554 | 36081 | 1528 |
|
gene | NA | NA | ENSG00000237613 | FAM138A | ensembl_havana | NA | 2 | ensembl_havana | lincRNA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| 1 | 52473 | 54936 | 2464 |
|
gene | NA | NA | ENSG00000268020 | OR4G4P | ensembl_havana | NA | 2 | ensembl_havana | pseudogene | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |