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 |
append_ynorm |
append_ynorm |
applySpline |
applies a spline smoothing to a tidy data.table containing x and y values. |
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. |
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 |
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. Mainly a utility function for loading MACS2 narrowPeak and broadPeak. |
easyLoad_broadPeak |
easyLoad_broadPeak takes a character vector of file paths to narrowPeak files from MACS2 and returns a named list of GRanges. |
easyLoad_narrowPeak |
easyLoad_narrowPeak takes a character vector of file paths to narrowPeak files from MACS2 and returns a named list of 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 |
prepare_fetch_GRanges |
prepares GRanges for windowed fetching. |
quantileGRangesWidth |
Quantile width determination strategy |
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 |
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 |
ssvFeatureVenn |
ggplot implementation of vennDiagram from limma package. currently limited at 3 sets |
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. |
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 |
ssvSignalHeatmap |
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 |
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. |