predictNMD: Predict NMD sensitivity on mRNA transcripts

In fursham-h/factR: Functional Annotation of Custom Transcriptomes

Predict NMD sensitivity on mRNA transcripts

Description

Predict NMD sensitivity on mRNA transcripts

Usage

predictNMD(x, ..., cds = NULL, NMD_threshold = 50, progress_bar = TRUE)

Arguments

x	Can be a GRanges object containing exon and CDS transcript features in GTF format. Can be a GRangesList object containing exon features for a list of transcripts.If so, 'cds' argument have to be provided. Can be a GRanges object containing exon features for a transcript. If so, 'cds' argument have to be provided.
...	Logical conditions to pass to dplyr::filter to subset transcripts for analysis. Variables are metadata information found in 'x' and multiple conditions can be provided delimited by comma. Example: transcript_id == "transcript1"
cds	If 'x' is a GRangesList object, 'cds' has to be a GRangesList containing CDS features for the list of transcripts in 'x'. List names in 'x' and 'cds' have to match. If 'x' is a GRanges object, 'cds' has to be a GRanges containing CDS features for the transcript in 'x'.
NMD_threshold	Minimum distance of stop_codon to last exon junction (EJ) which triggers NMD. Default = 50bp
progress_bar	Whether to display progress Default = TRUE

Value

Dataframe with prediction of NMD sensitivity and NMD features:

is_NMD: logical value in prediciting transcript sensitivity to NMD

stop_to_lastEJ: Integer value of the number of bases between the first base of the stop_codon to the last base of EJ. A positive value indicates that the last EJ is downstream of the stop_codon.

num_of_down_EJs: Number of EJs downstream of the stop_codon.

‘3_UTR_length': Length of 3’ UTR

Author(s)

Fursham Hamid

Examples

## ---------------------------------------------------------------------
## EXAMPLE USING SAMPLE DATASET
## ---------------------------------------------------------------------

# Load datasets
data(new_query_gtf, query_exons, query_cds)

## Using GTF GRanges as input
predictNMD(new_query_gtf)

### Transcripts for analysis can be subsetted using logical conditions
predictNMD(new_query_gtf, transcript_id == "transcript1")
predictNMD(new_query_gtf, 
transcript_id %in% c("transcript1", "transcript3"))


## Using exon and CDS GRangesLists as input
predictNMD(query_exons, cds = query_cds)
predictNMD(query_exons, cds = query_cds, transcript_id == "transcript3")


## Using exon and CDS GRanges as input
predictNMD(query_exons[[3]], cds = query_cds[[3]])



## ---------------------------------------------------------------------
## EXAMPLE USING TRANSCRIPT ANNOTATION
## ---------------------------------------------------------------------

library(AnnotationHub)

## Retrieve GRCm38 trancript annotation
ah <- AnnotationHub()
GRCm38_gtf <- ah[["AH60127"]]

## Run tool on specific gene family
predictNMD(GRCm38_gtf, gene_name == "Ptbp1")

fursham-h/factR documentation built on Aug. 20, 2023, 1:58 p.m.