Get the read coverages for each transcript in the BAM file (or a GAlignments object).
The read coverages are sampled at 100 positions along the transcript, and the coverage is scaled
by dividing the coverage at each position by the total read counts for the transcript. If a BAM
file is provided, alignment with MAPQ < 5, secondary alignments and supplementary alignments
are filtered out. A GAlignments
object can also be provided in case alternative filtering
is desired.
Value
a tibble of the transcript information and coverages, with the following columns:
transcript
: the transcript name / IDread_counts
: the total number of aligments for the transcriptcoverage_1-100
: the coverage at each of the 100 positions along the transcripttr_length
: the length of the transcript
Examples
ppl <- example_pipeline("BulkPipeline")
#> Writing configuration parameters to: /tmp/RtmpgpEV0i/file25bfed204dd/config_file_9663.json
#> Configured steps:
#> genome_alignment: TRUE
#> isoform_identification: TRUE
#> read_realignment: TRUE
#> transcript_quantification: TRUE
#> samtools not found, will use Rsamtools package instead
ppl@steps["isoform_identification"] <- FALSE
ppl <- run_step(ppl, "read_realignment")
#> Running step: read_realignment
#> Using reference annotation for transcriptome assembly.
#> Import genomic features from the file as a GRanges object ...
#> OK
#> Prepare the 'metadata' data frame ...
#> OK
#> Make the TxDb object ...
#> Warning: The "phase" metadata column contains non-NA values for features of type
#> stop_codon. This information was ignored.
#> Warning: genome version information is not available for this TxDb object
#> OK
#> Realigning sample sample1 -> /tmp/RtmpgpEV0i/file25bfed204dd/sample1_realign2transcript.bam
#> Warning: samtools not found, using Rsamtools instead, this could be slower and might fail for large BAM files.
#> Skipped sorting BAM files.
#> Realigning sample sample2 -> /tmp/RtmpgpEV0i/file25bfed204dd/sample2_realign2transcript.bam
#> Warning: samtools not found, using Rsamtools instead, this could be slower and might fail for large BAM files.
#> Skipped sorting BAM files.
#> Realigning sample sample3 -> /tmp/RtmpgpEV0i/file25bfed204dd/sample3_realign2transcript.bam
#> Warning: samtools not found, using Rsamtools instead, this could be slower and might fail for large BAM files.
#> Skipped sorting BAM files.
x <- get_coverage(ppl@transcriptome_bam[[1]])
head(x)
#> # A tibble: 1 × 103
#> transcript coverage_1 coverage_2 coverage_3 coverage_4 coverage_5 coverage_6
#> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 ENSMUST0000… 0.880 1 1 1 1 1
#> # ℹ 96 more variables: coverage_7 <dbl>, coverage_8 <dbl>, coverage_9 <dbl>,
#> # coverage_10 <dbl>, coverage_11 <dbl>, coverage_12 <dbl>, coverage_13 <dbl>,
#> # coverage_14 <dbl>, coverage_15 <dbl>, coverage_16 <dbl>, coverage_17 <dbl>,
#> # coverage_18 <dbl>, coverage_19 <dbl>, coverage_20 <dbl>, coverage_21 <dbl>,
#> # coverage_22 <dbl>, coverage_23 <dbl>, coverage_24 <dbl>, coverage_25 <dbl>,
#> # coverage_26 <dbl>, coverage_27 <dbl>, coverage_28 <dbl>, coverage_29 <dbl>,
#> # coverage_30 <dbl>, coverage_31 <dbl>, coverage_32 <dbl>, …