Package 'BREW3R.r'

Add new exons

Description

A function that from 2 GRanges add exons from the second one to the first one if the 3p of the last exon of the transcript in the first GRanges matches the 3p of an exon in the second one

Usage

add_new_exons(input_gr_to_extend, input_gr_with_new_exons)

Arguments

input_gr_to_extend	A GRanges to be complemented
input_gr_with_new_exons	A GRanges with exons to be added to the first one (exons with strand '*' are excluded)

Details

Potential new exons will be filtered for collision with exons present in the first GRanges even if they belong to the same gene_id. For the moment all potential exons extensions are added to the same existing transcript_id so introns maybe artificial introns.

Value

A GRanges identical to 'input_gr_to_extend' with new exons whose 'exon_id' contains BREW3R. 'exon_number' may have changed.

---

Adjust for collision

Description

A function that from a GRanges with 'old_width' Change the starts and ends to prevent collisions larger than with old coordinates

Usage

adjust_for_collision(input_gr)

Arguments

input_gr

A GRanges with 1 meta: 'old_width'

Value

A list with: - 'pot_issues': A dataframe with exons which overlaps between 'input_gr' and itself while gene_ids are different - 'new_gr': A GRanges identical to 'input_gr' except that start/end have been adjusted to prevent collisions.

---

Display debug messages if verbose allows it

Description

A function that extend rlang::inform to display a message if the verbose is at "debug" and show content of the variable

Usage

debug_msg(message = NULL, ...)

Arguments

message	String to display
...	Other parameters for rlang::inform

Value

Nothing

---

Extend GRanges

Description

A function that from a GRanges from gtf will extend the 3' of transcripts using another GRanges from gtf as a template

Usage

extend_granges(
  input_gr_to_extend,
  input_gr_to_overlap,
  extend_existing_exons = TRUE,
  add_new_exons = TRUE,
  overlap_resolution_fn = NULL
)

Arguments

input_gr_to_extend	A GRanges to extend (only exons are kept and strand * are excluded)
input_gr_to_overlap	A GRanges with intervals to overlap
extend_existing_exons	A boolean that indicates if existing exons should be extended
add_new_exons	A boolean that indicates if new exons with compatible splicing event should be added
overlap_resolution_fn	A file path where the dataframe giving details on the collision resolution is written

Details

During the extension process a special care is taking to prevent extension which would lead to overlap between different gene_ids.

Value

A GRanges based on 'input_gr_to_extend' where exons are extended and new exons can be added. Exons extended will have a '.ext' suffix to the original exon_id. Exons added will have a exon_id starting with 'BREW3R'.

Examples

# Very simple case
# input_gr:      ------->           ----->
# to_overlap:  ------------------>

# output:        ---------------->  ----->

input_gr <- GenomicRanges::GRanges(
    seqnames = "chr1",
    ranges = IRanges::IRanges(
        start = c(5, 20),
        end = c(10, 30)
    ),
    strand = "+",
    gene_id = c("gene1", "gene2"),
    transcript_id = c("transcript1", "transcript2"),
    type = "exon",
    exon_id = c("exon1", "exon2")
)

input_gr_to_overlap <- GenomicRanges::GRanges(
    seqnames = "chr1",
    ranges = IRanges::IRanges(
        start = 3,
        end = 15
    ),
    strand = "+",
    gene_id = "geneA",
    transcript_id = "transcriptA",
    type = "exon",
    exon_id = "exonA"
)

extend_granges(input_gr, input_gr_to_overlap)

---

Overlap exons and extend three prime end

Description

A function that from 2 GRanges returns a subset of the first GRanges which have been extended using the second GRanges

Usage

extend_using_overlap(input_gr_to_extend, input_gr_to_overlap)

Arguments

input_gr_to_extend	A GRanges with exons to extend (strand * are excluded)
input_gr_to_overlap	A GRanges with intervals to overlap

Value

A GRanges which is a subset of 'input_gr_to_extend' where 3' end have been modified to match the 3' end of 'input_gr_to_overlap' if they overlap (initial width have been stored into old_width)

---

Extract last exons

Description

A function that from a GRanges from gtf select only entries for the last exons If multiple exons overlap the last base of the grouping_variable, they will all be reported.

Usage

extract_last_exons(
  input_gr,
  grouping_variable = "transcript_id",
  invert = FALSE
)

Arguments

input_gr	A GRanges from a gtf
grouping_variable	A string with the name of the metadata which should be used to group
invert	A boolean that indicates if you want all except the last exons

Value

A GRanges which contains a subset of 'input_gr'

---

Filter new exons for collision

Description

A function that from 2 GRanges filter exons from the first one so they do not go three prime to the first collision with the second one.

Usage

filter_new_exons(all_exons_interesting, input_gr_to_extend)

Arguments

all_exons_interesting	A GRanges with exons to trim and filter
input_gr_to_extend	A GRanges to overlap

Value

A GRanges subset of 'all_exons_interesting'

---

Get five prime position

Description

A function that from a GRanges gives the 5' position

Usage

five_prime_pos(input_gr)

Arguments

input_gr

A GRanges or GRangeList

Value

A vector of integers

---

Get overlaps from different genes

Description

A function that from 2 GRanges generates a dataframe With queryHits, subjectHits when the gene_id is different

Usage

overlap_different_genes(gr1, gr2)

Arguments

gr1	A GRanges with 'gene_id'
gr2	A GRanges with 'gene_id'

Value

a data.frame with overlaps between gr1 and gr2 when gene_id from gr1 is different from gene_id from gr2. The data.frame has 4 columns: 'queryHits', 'subjectHits', 'query_gene_id' and 'subject_gene_id'

---

Display progression messages if verbose allows it

Description

A function that extend rlang::inform to display a message if the verbose is at "debug" or "progression"

Usage

progression_msg(...)

Arguments

...	Parameters for rlang::inform

Value

Nothing

---

Get three prime position

Description

A function that from a GRanges gives the 3' position

Usage

three_prime_pos(input_gr)

Arguments

input_gr

A GRanges or GRangeList

Value

A vector of integers

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