get_JunctionSeq_params: Formats Snapcount results in a form that can be easily passed...

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

Description

This allows for the visualization of junction counts along with their associated gene and exon counts in the context of a gene model. Performance is dependent on the total number of junctions and the length of the gene model i.e. larger gene regions may either completely fail to draw or take too long to be visualized.

Usage

get_JunctionSeq_params(query_builders, group_names, gene, sample_names = NULL)

output_example_function_calls(js_params)

Arguments

query_builders	A list of 1 of more QueryBuilder objects.
group_names	A vector of strings representing tissue groups.
gene	The name of the gene to match with the exon and gene query results.
sample_names	A vector of strings representing sample names.
js_params	An object returned from call to get_JunctionSeq_params.

Value

get_JunctionSeq_params returns an object containing the necessary parameters needed by calls to JunctionSeq::readJunctionSeqCounts and JunctionSeq::plotJunctionSeqResultsForGene.

output_example_function_calls outputs the necessary JunctionSeq calls needed to produce a plot.

Examples

## Not run: 
sb1 <- QueryBuilder(compilation = "gtex", regions = "chr7:128393029-128394277")
sb1 <- set_row_filters(sb1, contains == 1, coverage_sum >= 1000)
sb1 <- set_column_filters(sb1, SMTS == "Brain")

sb2 <- set_column_filters(sb1, SMTS == "Pituitary")

sb3 <- set_column_filters(sb2, SMTS == "Spleen")

js <- get_JunctionSeq_params(
    query_builders = list(sb1, sb2, sb3),
    gene = "IMPDH1",
    group_names = list("Brain", "Pituitary", "Spleen")
)

output_example_function_calls(js)

## End(Not run)

snapcount documentation built on Nov. 8, 2020, 4:53 p.m.