ChIPtSNE.runTSNE: ChIPtSNE.runTSNE

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

ChIPtSNE.runTSNE

Description

ChIPtSNE.runTSNE

Usage

ChIPtSNE.runTSNE(sts)

Arguments

sts	A valid ChIPtSNE object, needs ssvQC.prepSignal to be called.

Value

A valid ChIPtSNE object with t-SNE called and ready for plots.

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)

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