grFromCohortDf: Extract GRange objects from cohort exon expression data
In jefferys/fusionExpressionPlot: Plot Expression Profiles for Fused Genes

Description Usage Arguments Value Cohort exon expression data

Given a dataframe describing exon expression for a sample cohort, generate a list of GRange objects for one sample, by selected genes. Each GRange object is identified by gene name and includes a meta-data column giving the expression data.

1	grFromCohortDf(df, genes, sample, column = "exonData")

`df`	A dataframe with gene model and exon expression. Required to have the following columns: 'chr', 'start', 'end', 'strand', 'gene', and one column for each sample.
`genes`	The names of the genes to extract from the cohort data frame.
`sample`	The name of the sample to extract from the df. Required
`column`	The metadata column name under which the expression data is added to the GRange objects. By default this is 'exonData'

A List of GRanges object for the gene, with start and end positions of the exon specified, and with a metadata column "relativeExpression" giving the relative expression for the selected gene in the selected sample.

The input dataframe must have the following columns:

chr: The chromosome this exon is on, as 'chr1'...'chr22', chrX', 'chrY', or 'chrM'.
start: The position of the first base of the exon.
end: The position of the last base of the exon.
strand: The strand of this exon (+,-, or *). All exons in a gene should have the same strand.
gene: The name of this gene. All exons in a gene should have the same name, and no exons from different genes should have the same name.
***: The normalized expression value for this exon in sample named "***". Should have one column for every sample in the cohort. Sample names may not be "chr", "start", "end", "strand", "gene", and must be unique.

Start and end are assumed to be 1 based, but this does not really matter as long as all positions here and in any position data (i.e. fusions) used with this data all have the same base.

jefferys/fusionExpressionPlot documentation built on May 19, 2019, 3:59 a.m.