Visualization and annotation of read signal over genomic ranges with profileplyr


[Up] [Top]

Documentation for package ‘profileplyr’ version 1.3.3

Help Pages

annotateRanges Annotate profileplyr ranges to genes using ChIPseeker
annotateRanges-method Annotate profileplyr ranges to genes using ChIPseeker
annotateRanges_great Annotate profileplyr ranges to genes using rGREAT
annotateRanges_great-method Annotate profileplyr ranges to genes using rGREAT
as_profileplyr Import ChIPprofile object to profileplyr
BamBigwig_to_chipProfile BamBigwig_to_chipProfile
c-method Join, subset and manipulate ChIPprofile objects
clusterRanges Cluster Ranges
clusterRanges-method Cluster Ranges
convertToEnrichedHeatmapMat export a profileplyr object to a list of matrices that can be used as an input for EnrichedHeatmap
convertToEnrichedHeatmapMat-method 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
export_deepToolsMat-method Export and import profileplyr from/to deeptools
generateEnrichedHeatmap generateEnrichedHeatmap
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
groupBy group the rows and ranges of the profileplyr object
groupBy-method group the rows and ranges of the profileplyr object
import_deepToolsMat Export and import profileplyr from/to deeptools
inherit_group_function Redundant code for inheriting grouping wrapped into subsetbyRangeOverlap() or subsetbyGeneListOverlap() functions
K27ac_GRlist_hind_liver_top5000 GRangesList of the top 5000 H3K27ac peaks from hindbrain and liver downloaded from ENCODE
orderBy choose the column by which to order the ranges by within each group
orderBy-method 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
sampleData Retrieve and set sample data in profileplyr object
sampleData-method Retrieve and set sample data in profileplyr object
sampleData<- Retrieve and set sample data in profileplyr object
sampleData<--method Retrieve and set sample data in profileplyr object
subsetbyGeneListOverlap Subset ranges based on overlap with lists of Gene sets
subsetbyRangeOverlap Subset ranges based on overlap with a GRanges object
subset_GR_GL_common_top Redundant code wrapped into subsetbyRangeOverlap() or subsetbyGeneListOverlap() functions
summarize summarize the rows of a deepTools matrix
summarize-method summarize the rows of a deepTools matrix
[-method Join, subset and manipulate ChIPprofile objects