shared_sample_counts: Shared Sample Count (SSC): counts total number of samples in...

In langmead-lab/snapcount: R/Bioconductor Package for interfacing with Snaptron for rapid querying of expression counts

Shared Sample Count (SSC): counts total number of samples in which 2 different junctions both occur in.

Description

This produces a list of user-specified groups and the read coverage of the junctions in all the samples which were shared across all the basic queries occurring in each group.

Usage

shared_sample_counts(..., group_names = NULL)

Arguments

...	One or more lists of QueryBuilder objects
group_names	Optional vector of character strings representing group names

Details

Example: User defines a single group of junctions "GroupA" made up of 2 separate regions (two basic queries).

An SSC query will return a single line for GroupA which will have the total number of samples which had at least one junction which was returned from both basic queries. It will also report a summary statistic of the total number of groups which had one or more samples that were shared across the basic queries, in this case it would be 1. Also, it will report the number of groups which had at least one shared sample and which had matching junctions (from the query) which were fully annotated.

This function can be used to determine how much cross-sample support there is for a particular junction configuration (typically a cassette exon).

Value

A DataFrame of results based on the list of groups passed in via "group_names". Each group is reported with the # of unique samples which occurred in all of its defined set of related basic queries (e.g. two inclusion basic queries in a cassette exon scenario).

Examples

g1 <- QueryBuilder(compilation = "gtex", regions = "chr1:1879786-1879786")
g1 <- set_coordinate_modifier(g1, Coordinates$EndIsExactOrWithin)
g1 <- set_row_filters(g1, strand == "-")

g2 <- QueryBuilder(compilation = "gtex", regions = "chr1:1879903-1879903")
g2 <- set_coordinate_modifier(g2, Coordinates$StartIsExactOrWithin)
g2 <- set_row_filters(g2, strand == "-")

ssc<-shared_sample_counts(list(g1, g2))

langmead-lab/snapcount documentation built on May 1, 2022, 4:27 a.m.