BamBigwig_to_chipProfile
                        BamBigwig_to_chipProfile
ChIPprofile-class       ChIPprofile S4 class
K27ac_GRlist_hind_liver_top5000
                        GRangesList of the top 5000 H3K27ac peaks from
                        hindbrain and liver downloaded from ENCODE
annotateRanges          Annotate profileplyr ranges to genes using
                        ChIPseeker
annotateRanges_great    Annotate profileplyr ranges to genes using
                        rGREAT
as_profileplyr          Import ChIPprofile object to profileplyr
c,ChIPprofile-method    Combine ChIPprofile objects
chipExampleBig          Example ChIPprofile object
clusterRanges           Cluster Ranges
convertToEnrichedHeatmapMat
                        export a profileplyr object to a list of
                        matrices that can be used as an input for
                        EnrichedHeatmap
export_deepToolsMat     Export and import profileplyr from/to deeptools
gene_list_character     Character vector of the top differentially
                        expressed genes from hindbrain versus liver as
                        measured by RNA-seq
gene_list_dataframe     Dataframe of top differentially expressed genes
                        from hindbrain versus liver as measured by
                        RNA-seq
generateEnrichedHeatmap
                        generateEnrichedHeatmap
generateProfilePlot     Import ChIPprofile object to profileplyr
groupBy                 group the rows and ranges of the profileplyr
                        object
ik_Profiles             Example ChIPprofile object (Ikaros profiles)
inherit_group_function
                        Redundant code for inheriting grouping wrapped
                        into subsetbyRangeOverlap() or
                        subsetbyGeneListOverlap() functions
orderBy                 choose the column by which to order the ranges
                        by within each group
params                  Retrieve and set parameters in profileplyr
                        object
profileplyr-class       Join, subset and manipulate ChIPprofile objects
pwmToCoverage           PWM hits as an RleList
sampleData              Retrieve and set sample data in profileplyr
                        object
subset_GR_GL_common_top
                        Redundant code wrapped into
                        subsetbyRangeOverlap() or
                        subsetbyGeneListOverlap() functions
subsetbyGeneListOverlap
                        Subset ranges based on overlap with lists of
                        Gene sets
subsetbyRangeOverlap    Subset ranges based on overlap with a GRanges
                        object
summarize               summarize the rows of a deepTools matrix
