map_requant: Maps the re-quantification result from EasyQuant. on the...

In TRON-Bioinformatics/splice2neo: Aberrant splice junction analysis with associated mutations

Maps the re-quantification result from EasyQuant. on the junction-transcript centric tibble by hash id.

Description

Maps the re-quantification result from EasyQuant. on the junction-transcript centric tibble by hash id.

Usage

map_requant(path_to_easyquant_folder, junc_tib)

Arguments

path_to_easyquant_folder	The path to EasyQuant folder
junc_tib	The junction-transcript centric tibble, i.e. each row represents an altered transcript. Must contain a column hash_id with hash ids that relate to the column name in the Easyquant output.

Value

Extended junction-transcript tibble with re-quantification results by Easyquant. More details about Easyquant can be obtained at https://github.com/TRON-Bioinformatics/easyquant The following columns are added:

• junc_interval_start: Junction reads overlapping the junction of interest. In case of intron retentions, junctions reads that overlap the start of the intron retention interval.

• junc_interval_end: In case of intron retentions, junctions reads that overlap the end of the intron retention interval. Is NA for non intron retention events.

• span_interval_start: Spanning pairs overlapping the junction of interest. In case of intron retentions, spanning pairs that overlap the start of the intron retention interval.

• span_interval_end: In case of intron retentions, spanning pairs that overlap the end of the intron retention interval. Is NA for non intron retention events.

• within_interval: Number of reads that map into the intron retention interval. Is NA for non intron retention events.

• within_interval_left: Number of reads that map into interval left to the intron retention or splice junction of interest.

• within_interval_right: Number of reads that map into interval right of the intron retention or splice junction of interest.

• coverage_perc: Intron retention interval coverage defined as the percentage of the given interval that is covered by reads. Is NA for non intron retention events.

• coverage_perc_left: Interval coverage defined as the percentage of the interval left to the intron retention or splice junction of interest that is covered by reads.

• coverage_perc_right: Interval coverage defined as the percentage of the interval right to the intron retention or splice junction of interest that is covered by reads.

• coverage_mean: Interval coverage defined as the mean number of reads covering a position in the given interval representing an intron retention. Is NA for non intron retention events.

• coverage_mean_left: Interval coverage defined as the mean number of reads covering a position in the interval left to the intron retention or splice junction of interest.

• coverage_mean_right: Interval coverage defined as the mean number of reads covering a position in the interval right to the intron retention or splice junction of interest.

• coverage_median: Interval coverage defined as the median number of reads covering a position in the given interval representing an intron retention. Is NA for non intron retention events.

• coverage_median_left: Interval coverage defined as the median number of reads covering a position in the interval left to the intron retention or splice junction of interest.

• coverage_median_right: Interval interval coverage defined as the median number of reads covering a position in the interval right to the intron retention or splice junction of interest.

TRON-Bioinformatics/splice2neo documentation built on July 27, 2024, 3:25 a.m.