# Set Based Visualizations for Next-Gen Sequencing Data

## Documentation for package ‘seqsetvis’ version 1.16.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

seqsetvis-package | easy awesome peak set vis TESTING seqsetvis allows you to...
.expand_cigar_dt | Expand intermediate bam fetch by cigar codes
.expand_cigar_dt_recursive | Expand intermediate bam fetch by cigar codes
.rm_dupes | Remove duplicate reads based on stranded start position. This is an over-simplification. For better duplicate handling, duplicates must be marked in bam and flag passed to fetchBam() ... for ScanBamParam
.rm_dupesPE | Remove duplicate paired-end reads based on start and end position. This is an over-simplification. For better duplicate handling, duplicates must be marked in bam and flag passed to fetchBamPE() ... for ScanBamParam
add_cluster_annotation | add_cluster_annotation
append_ynorm | append_ynorm
applySpline | applies a spline smoothing to a tidy data.table containing x and y values.
assemble_heatmap_cluster_bars | assemble_heatmap_cluster_bars
Bcell_peaks | 4 random peaks for paired-end data
calc_norm_factors | calc_norm_factors
centerAtMax | centers profile of x and y. default is to center by region but across all samples.
centerFixedSizeGRanges | Transforms set of GRanges to all have the same size.
centerGRangesAtMax | Centers query GRanges at maximum signal in prof_dt.
chromHMM_demo_bw_states_gr | MCF10A CTCF profiles at 20 windows per chromHMM state, hg38.
chromHMM_demo_chain_url | URL to download hg19ToHg38 liftover chain from UCSC
chromHMM_demo_data | chromHMM state segmentation in the MCF7 cell line
chromHMM_demo_overlaps_gr | overlap of MCF10A CTCF with MCF7 chromHMM states, hg38.
chromHMM_demo_segmentation_url | URL to download hg19 MCF7 chromHMM segmentation
chromHMM_demo_state_colors | original state name to color mappings stored in segmentation bed
chromHMM_demo_state_total_widths | state name to total width mappings, hg38
clusteringKmeans | perform kmeans clustering on matrix rows and return reordered matrix along with order matched cluster assignments. clusters are sorted using hclust on centers
clusteringKmeansNestedHclust | perform kmeans clustering on matrix rows and return reordered matrix along with order matched cluster assignments clusters are sorted using hclust on centers the contents of each cluster are sorted using hclust
col2hex | converts a valid r color name ("black", "red", "white", etc.) to a hex value
collapse_gr | collapse_gr
convert_collapsed_coord | convert_collapsed_coord
crossCorrByRle | Calculate cross correlation by using shiftApply on read coverage Rle
CTCF_in_10a_bigWig_urls | FTP URL path for vignette data.
CTCF_in_10a_data | CTCF ChIP-seq in breast cancer cell lines
CTCF_in_10a_narrowPeak_grs | list of GRanges that results in 100 random subset when overlapped
CTCF_in_10a_narrowPeak_urls | FTP URL path for vignette data. from
CTCF_in_10a_overlaps_gr | 100 randomly selected regions from overlapping CTCF peaks in 10a cell ChIP-seq
CTCF_in_10a_profiles_dt | Profiles for 100 randomly selected regions from overlapping CTCF peaks in 10a cell ChIP-seq Results from fetching bigwigs with CTCF_in_10a_overlaps_gr.
CTCF_in_10a_profiles_gr | Profiles for 100 randomly selected regions from overlapping CTCF peaks in 10a cell ChIP-seq Results from CTCF_in_10a_overlaps_gr
easyLoad_bed | easyLoad_bed takes a character vector of file paths to bed plus files and returning named list of GRanges.
easyLoad_broadPeak | easyLoad_broadPeak takes a character vector of file paths to narrowPeak files from MACS2 and returns a named list of GRanges.
easyLoad_FUN | easyLoad_FUN takes a character vector of file paths run an arbitrary function defined in load_FUN
easyLoad_IDRmerged | easyLoad_IDRmerged loads "overlapped-peaks.txt" from IDR.
easyLoad_narrowPeak | easyLoad_narrowPeak takes a character vector of file paths to narrowPeak files from MACS2 and returns a named list of GRanges.
easyLoad_seacr | easyLoad_seacr takes a character vector of file paths to seacr output bed files and returns a named list of GRanges.
expandCigar | Expand cigar codes to GRanges
fetchBam | fetch a bam file pileup with the ability to consider read extension to fragment size (fragLen)
fragLen_calcStranded | calculate fragLen from a bam file for specified regions
fragLen_fromMacs2Xls | parse fragLen from MACS2 output
getReadLength | determine the most common read length for input bam_file. uses 50 randomly selected regions from query_gr. If fewer than 20 reads are present, loads all of query_gr.
ggellipse | returns a ggplot with ellipses drawn using specified parameters used by ssvFeatureVenn and ssvFeatureEuler
harmonize_seqlengths | harmonize_seqlengths
make_clustering_matrix | make_clustering_matrix
merge_clusters | merge_clusters
prepare_fetch_GRanges | prepares GRanges for windowed fetching.
prepare_fetch_GRanges_names | Creates a named version of input GRanges using the same method seqsetvis uses internally to ensure consistency.
prepare_fetch_GRanges_width | prepares GRanges for windowed fetching.
quantileGRangesWidth | Quantile width determination strategy
reorder_clusters_hclust | reorder_clusters_hclust
reorder_clusters_manual | reorder_clusters_manual
reorder_clusters_stepdown | reorder_clusters_stepdown
reverse_clusters | reverse_clusters
safeBrew | allows RColorBrew to handle n values less than 3 and greater than 8 without warnings and return expected number of colors.
seqsetvis | easy awesome peak set vis TESTING seqsetvis allows you to...
set_list2memb | convert a list of sets, each list item should be a character vector denoting items in sets
shift_anchor | orients the relative position of x's zero value and extends ranges to be contiguous
split_cluster | split_cluster
ssvConsensusIntervalSets | Intersect a list of GRanges to create a single GRanges object of merged ranges including metadata describing overlaps per input GRanges.
ssvFactorizeMembTable | Convert any object accepted by ssvMakeMembTable to a factor To avoid ambiguity,
ssvFeatureBars | bar plots of set sizes
ssvFeatureBinaryHeatmap | binary heatmap indicating membership. heatmap is sorted by column left to right. change column order to reveal patterns
ssvFeatureEuler | Try to load a bed-like file and convert it to a GRanges object
ssvFeaturePie | pie plot of set sizes
ssvFeatureUpset | ssvFeatureUpset
ssvFeatureVenn | ggplot implementation of vennDiagram from limma package. currently limited at 3 sets. ssvFeatureUpset and ssvFeatureBinaryHeatmap are good options for more than 3 sets. ssvFeatureEuler can work too but can take a very long time to run for more than 5 or so.
ssvFetchBam | Iterates a character vector (ideally named) and calls 'ssvFetchBam.single' on each. Appends grouping variable to each resulting data.table and uses rbindlist to efficiently combine results
ssvFetchBam.single | fetch a windowed version of a bam file, returns GRanges
ssvFetchBamPE | ssvFetchBam for paired-end ChIP-seq files. Only concordant reads are considered, but this has been minimally tested, please verify.
ssvFetchBamPE.single | fetch a windowed version of a paired-end bam file, returns GRanges In contrast to ssvFetchBam, extension of reads to estimated fragment size is not an issue as each read pair represents a fragment of exact size.
ssvFetchBigwig | Iterates a character vector (ideally named) and calls 'ssvFetchBigwig.single' on each. Appends grouping variable to each resulting data.table and uses rbindlist to efficiently combine results.
ssvFetchBigwig.single | Fetch values from a bigwig appropriate for heatmaps etc.
ssvFetchGRanges | Fetch coverage values for a list of GRanges.
ssvFetchSignal | signal loading framework
ssvMakeMembTable | generic for methods to convert various objects to a logical matrix indicating membership of items (rows) in sets (columns)
ssvMakeMembTable-method | generic for methods to convert various objects to a logical matrix indicating membership of items (rows) in sets (columns)
ssvOverlapIntervalSets | Intersect a list of GRanges to create a single GRanges object of merged ranges including metadata describing overlaps per input GRanges
ssvSignalBandedQuantiles | plot profiles from bigwigs
ssvSignalClustering | Clustering as for a heatmap. This is used internally by 'ssvSignalHeatmap' but can also be run before calling ssvSignalHeatmap for greater control and access to clustering results directly.
ssvSignalHeatmap | heatmap style representation of membership table. instead of clustering, each column is sorted starting from the left.
ssvSignalHeatmap.ClusterBars | heatmap style representation of membership table. instead of clustering, each column is sorted starting from the left.
ssvSignalLineplot | construct line type plots where each region in each sample is represented
ssvSignalLineplotAgg | aggregate line signals in a single line plot
ssvSignalScatterplot | maps signal from 2 sample profiles to the x and y axis. axes are standard or "volcano" min XY vs fold-change Y/X
ssv_mclapply | ssv_mclapply
test_peaks | 4 random peaks for single-end data and 4 control regions 30kb downstream from each peak.
viewGRangesWinSample_dt | get a windowed sampling of score_gr
viewGRangesWinSummary_dt | Summarizes signal in bins. The same number of bins per region in qgr is used and widths can vary in qgr, in contrast to 'viewGRangesWinSample_dt' where width must be constant across regions.
within_clust_sort | within_clust_sort