'importGH' imports the datadump.xlsx from https://genecards.weizmann.ac.il/geneloc/index.shtml and returns adjusted ghDB object
- @param: path, filepath on your system
- @return: ghDB, genehancer-DB import to work with
'queryGHdb' given a list of GH-regions with START/END coordinates this function maps variants in set to this list and creates a new column "GHID"
- @param: set, annotated list to be matched
- @param: GHdb, list of GH-regions with cols "GHID","CHROM","START","END"
- @return: set, input-set extended by "CandidateGene"-column
'matchGenehancers' given a list of names for gois this function finds all the regions in ghDB that are associated with those genes and outputs a reduced version of ghDB to work with in your project
- @param: query, list of gene names to match against
- @param: genehancer, imported dataframe of ghDB
- @return: tmpGH, ghDB reduced to goi
'evalGH' analyses cols 'CandidateGene' and 'GHID' and returns summary for input-set
- @param: input, annotated list (SV,CNV,INDEL,SNV)
- @param: ghDB, genehancer-DB object
- @return: summary object with cols 'Gene','scores','sum|max|minscores','nscores'
'topGGH' takes an evaluation object as input and returns a bar-plot object of the top genes of interest associated with GH-regions, i.e., most GH-regions
- @param: evalObj, output of 'evalGH' function
- @param: percent, displayed percentage of genes [0,1], defaults to 10% if left empty
- @param: plottitle, headline for this plot, may be left empty
- @return: p1, a ggplot2 prepped plot
'topGScore' takes an evaluation object as input and returns a bar-plot object of the top genes of interest based on max-score
- @param: evalObj, output of 'evalGH' function
- @param: percent, displayed percentage of genes [0,1]1], defaults to 10% if left empty
- @param: plottitle, headline for this plot, may be left empty
- @return: p1, a ggplot2 prepped plot
'topGDA' analyses cols 'CandidateGene' return plot of directly associated Cgenes
- @param: input, annotated list (SV,CNV,INDEL,SNV)
- @param: percent, displayed percentage of genes [0,1]1], defaults to 10% if left empty
- @param: plottitle, headline for this plot, may be left empty
- @return: p1, a ggplot2 prepped plot