Predict protein domain families from coding transcripts

Predict protein domain families from coding transcripts

predictDomains(x, fasta, ..., plot = FALSE, progress_bar = FALSE, ncores = 4)

Arguments

x

Can be a GRanges object containing 'CDS' features in GTF format

Can be a GRangesList object containing CDS ranges for each transcript

fasta

BSgenome or Biostrings object containing genomic sequence

...

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"

plot

Argument whether to plot out protein domains (Default: FALSE). Note: only first 20 proteins will be plotted

progress_bar

Argument whether to show progress bar (Default: FALSE). Useful to track progress of predicting a long list of proteins.

ncores

Number of cores to utilise to perform prediction

Value

Dataframe containing protein features for each cds entry

Author

Fursham Hamid

Examples

## ---------------------------------------------------------------------
## EXAMPLE USING SAMPLE DATASET
## ---------------------------------------------------------------------
# Load Mouse genome sequence
library(BSgenome.Mmusculus.UCSC.mm10)

# Load dataset
data(new_query_gtf)

# predict domains of all CDSs in query GTF
predictDomains(new_query_gtf, Mmusculus, ncores=1)
#> Checking CDSs and translating protein sequences
#> Predicting domain families for 4 proteins
#> # A tibble: 14 × 5
#>    transcript  description             eval     begin   end
#>    <chr>       <chr>                   <chr>    <dbl> <dbl>
#>  1 transcript1 RNA-binding domain, RBD 1.54e-20    46   143
#>  2 transcript1 RNA-binding domain, RBD 1.54e-20   357   446
#>  3 transcript1 RNA-binding domain, RBD 1.54e-20   177   281
#>  4 transcript1 RNA-binding domain, RBD 1.54e-20   469   553
#>  5 transcript2 RNA-binding domain, RBD 1.54e-20    46   143
#>  6 transcript2 RNA-binding domain, RBD 1.54e-20   331   420
#>  7 transcript2 RNA-binding domain, RBD 1.54e-20   177   281
#>  8 transcript2 RNA-binding domain, RBD 1.54e-20   443   527
#>  9 transcript3 RNA-binding domain, RBD 1.54e-20    46   143
#> 10 transcript3 RNA-binding domain, RBD 1.54e-20   177   281
#> 11 transcript4 RNA-binding domain, RBD 1.54e-20   291   380
#> 12 transcript4 RNA-binding domain, RBD 1.54e-20   137   241
#> 13 transcript4 RNA-binding domain, RBD 1.54e-20    39    95
#> 14 transcript4 RNA-binding domain, RBD 1.54e-20   403   487

# predict domains of CDSs from Ptbp1 gene
predictDomains(new_query_gtf, Mmusculus, gene_name == "Ptbp1",ncores=1)
#> Checking CDSs and translating protein sequences
#> Predicting domain families for 4 proteins
#> # A tibble: 14 × 5
#>    transcript  description             eval     begin   end
#>    <chr>       <chr>                   <chr>    <dbl> <dbl>
#>  1 transcript1 RNA-binding domain, RBD 1.54e-20    46   143
#>  2 transcript1 RNA-binding domain, RBD 1.54e-20   357   446
#>  3 transcript1 RNA-binding domain, RBD 1.54e-20   177   281
#>  4 transcript1 RNA-binding domain, RBD 1.54e-20   469   553
#>  5 transcript2 RNA-binding domain, RBD 1.54e-20    46   143
#>  6 transcript2 RNA-binding domain, RBD 1.54e-20   331   420
#>  7 transcript2 RNA-binding domain, RBD 1.54e-20   177   281
#>  8 transcript2 RNA-binding domain, RBD 1.54e-20   443   527
#>  9 transcript3 RNA-binding domain, RBD 1.54e-20    46   143
#> 10 transcript3 RNA-binding domain, RBD 1.54e-20   177   281
#> 11 transcript4 RNA-binding domain, RBD 1.54e-20   291   380
#> 12 transcript4 RNA-binding domain, RBD 1.54e-20   137   241
#> 13 transcript4 RNA-binding domain, RBD 1.54e-20    39    95
#> 14 transcript4 RNA-binding domain, RBD 1.54e-20   403   487

# predict domains of CDSs from Ptbp1 gene and plot architecture out
predictDomains(new_query_gtf, Mmusculus, gene_name == "Ptbp1", plot = TRUE,ncores=1)
#> Checking CDSs and translating protein sequences
#> Predicting domain families for 4 proteins

#> # A tibble: 14 × 5
#>    transcript  description             eval     begin   end
#>    <chr>       <chr>                   <chr>    <dbl> <dbl>
#>  1 transcript1 RNA-binding domain, RBD 1.54e-20    46   143
#>  2 transcript1 RNA-binding domain, RBD 1.54e-20   357   446
#>  3 transcript1 RNA-binding domain, RBD 1.54e-20   177   281
#>  4 transcript1 RNA-binding domain, RBD 1.54e-20   469   553
#>  5 transcript2 RNA-binding domain, RBD 1.54e-20    46   143
#>  6 transcript2 RNA-binding domain, RBD 1.54e-20   331   420
#>  7 transcript2 RNA-binding domain, RBD 1.54e-20   177   281
#>  8 transcript2 RNA-binding domain, RBD 1.54e-20   443   527
#>  9 transcript3 RNA-binding domain, RBD 1.54e-20    46   143
#> 10 transcript3 RNA-binding domain, RBD 1.54e-20   177   281
#> 11 transcript4 RNA-binding domain, RBD 1.54e-20   291   380
#> 12 transcript4 RNA-binding domain, RBD 1.54e-20   137   241
#> 13 transcript4 RNA-binding domain, RBD 1.54e-20    39    95
#> 14 transcript4 RNA-binding domain, RBD 1.54e-20   403   487