merge_samples: Merge Samples

In rpolicastro/tsrexplorer: TSS and TSR Analysis

Description

Merge TSSs or TSRs by group or select samples.

Usage

merge_samples(
  experiment,
  data_type = c("tss", "tsr"),
  threshold = NULL,
  sample_sheet = NULL,
  merge_group = NULL,
  merge_list = NULL,
  max_distance = NULL,
  genome_assembly = NULL
)

Arguments

experiment	TSRexploreR object.
data_type	Merge TSSs ('tss') or TSRs ('tsr').
threshold	TSSs or TSRs with a score below this value will not be considered.
sample_sheet	A sample sheet data.frame or tab delimited file. Must have the columns 'sample_name', 'file_1', and 'file_2'. Additional meta-data columns can be added with sample information such as condition and batch.
merge_group	The name of the column in the sample sheet that has the factor levels to merge samples by.
merge_list	If merge_group is set to 'FALSE', specify what samples to merge in list format. List names will be the new TSS/TSR name, and the list contents should be a character vector of the TSSs or TSRs to merge.
max_distance	Merge TSRs within this distance.
genome_assembly	Genome assembly in FASTA or BSgenome format.

Details

This function will merge overlapping TSSs or TSRs from different samples using either the sample sheet or a named list. If 'merge_group' is specified, the new merged TSS/TSR set will be the factor level in the column, and all TSS/TSR sets sharing that factor level will be merged. If 'merge_list' is specified, the new TSS/TSR set will be the name of the list element, and the samples to merge will be a character vector as the list element.

'merge_distance' is provided for TSRs, and will merge TSRs within a certain distance from other TSRs.

Value

TSRexploreR object containing merged TSSs or TSRs.

Examples

data(TSSs)
sample_sheet <- data.frame(
  sample_name=sprintf("S288C_D_%s", seq_len(2)),
  file_1=rep(NA, 2), file_2=rep(NA, 2),
  condition="Diamide"
)
assembly <- system.file("extdata", "S288C_Assembly.fasta", package="TSRexploreR")

exp <- TSSs[seq_len(2)] %>%
  tsr_explorer(sample_sheet=sample_sheet, genome_assembly=assembly) %>%
  format_counts(data_type="tss")

exp <- merge_samples(exp, data_type="tss", merge_group="condition")

rpolicastro/tsrexplorer documentation built on Oct. 17, 2021, 3:02 p.m.