ChIPtSNE: ChIPtSNE

In jrboyd/seqtsne: Application of t-sne to NGS Genomic Signal Profiles

ChIPtSNE

Description

ChIPtSNE

Usage

ChIPtSNE(
  features_config = NULL,
  signal_config = NULL,
  out_dir = getwd(),
  bfc = NULL,
  perplexity = 50,
  n_glyphs_x = 8,
  n_glyphs_y = n_glyphs_x,
  n_heatmap_pixels_x = 25,
  n_heatmap_pixels_y = n_heatmap_pixels_x
)

Arguments

features_config	Controls features configuration. May be a: QcConfigFeatures object, path to a file defining configuration via QcConfigFeatures.parse, features files to define via QcConfigFeatures.files, or a data.frame to pass to QcConfigFeatures.
signal_config	Controls signal configuration. May be a: QcConfigSignal object, path to a file defining configuration via QcConfigSignal.parse, features files to define via QcConfigSignal.files, or a data.frame to pass to QcConfigSignal.
out_dir	NYI
bfc	BiocFileCache object to use for caching. If NULL, default new_cache() will be used.
perplexity	passed to Rtsne::Rtsne()
n_glyphs_x	number of glyphs across x-axis to summarize profiles in t-SNE space. Default is 8.
n_glyphs_y	number of glyphs across y-axis. Default is the same as n_glyphs_x.
n_heatmap_pixels_x	number of pixels to use in heatmap across x-axis in t-SNE space. Default is 25.
n_heatmap_pixels_y	number of pixels to use in heatmap across y-axis in t-SNE space. Default is same as n_heatmap_pixels_x.

Value

a valid ChIPtSNE object.

Examples

library(chiptsne)
library(ssvQC)
query_bed_file = system.file(package = "chiptsne", "extdata/query_gr.bed")
query_gr = rtracklayer::import.bed(query_bed_file)
bam_files = dir(system.file(package = "chiptsne", "extdata"), pattern = "bam$", full.names = TRUE)
qc_config_features = QcConfigFeatures.GRanges(query_gr)
qc_config_signal = QcConfigSignal.files(bam_files)
qc_config_signal$flip_signal_mode = SQC_FLIP_SIGNAL_MODES$high_on_left
qc_config_signal$center_signal_at_max = TRUE
sts = ChIPtSNE(qc_config_features, qc_config_signal)
sts = ChIPtSNE.runTSNE(sts)

sts$n_glyphs_x = 7
sts$n_glyphs_y = 5

sts$n_heatmap_pixels_x = 5
sts$n_heatmap_pixels_y = 9
sts.replot = ssvQC.plotSignal(sts)

sts$plots$TSNE$regional_glyphs$query_features$All_signal
sts.replot$plots$TSNE$regional_glyphs$query_features$All_signal

sts$plots$TSNE$regional_heatmap$query_features$All_signal
sts.replot$plots$TSNE$regional_heatmap$query_features$All_signal

jrboyd/seqtsne documentation built on Nov. 5, 2022, 6:37 a.m.