opening_act2: Standard analysis of ChIP-seq experiments
In hochwagenlab/hwglabr2: Collection of R functions used in the Hochwagen Lab

opening_act2

R Documentation

Standard analysis of ChIP-seq experiments

Description

Runs the lab's standard analysis of ChIP-seq experiment data and produces several .pdf files of analysis plots to be kept in a new folder at .../LabShare/HTGenomics/Opening_act/.

Usage

opening_act2(
  signal_data,
  genome,
  genotype,
  chip_target,
  sample_id,
  output_path = "/Volumes/LabShare/HTGenomics/Opening_act/",
  user_input = TRUE,
  run_chr_size_bias = TRUE,
  run_centromeres = TRUE,
  run_rDNA = TRUE,
  run_telomeres = TRUE,
  run_dsb_hotspots = TRUE,
  run_axis = TRUE,
  run_meta_orf = TRUE
)

Arguments

`signal_data`	Input signal track data as a `GRanges` object (see `?"GRanges-class"` for more details). To load wiggle and bedGraph data run `import_wiggle` and `import_bedGraph`, respectively. No default.
`genome`	Character object specifying the genome version; accepts one of the following options: `"SK1Yue"` `"sacCer3"` No default.
`genotype`	Character object indicating the relevant strain mutations. Just use `genotype=WT`, for example, if there are no relevant mutations. No default.
`chip_target`	Character object indicating the ChIP target protein. No default.
`sample_id`	Character object indicating the sample ID, including the ID used in the analysis pipeline (with a date) and the read mapping conditions (see examples below). If `user_input=TRUE` the function asks the user to check that the provided `sample_id` matches the required format before proceeding with the analysis. No default.
`output_path`	Character object with a valid path to directory to save output files at. Defaults to `'/Volumes/LabShare/HTGenomics/Opening_act/'`. Defaults to `output_path='/Volumes/LabShare/HTGenomics/Opening_act/'`
`user_input`	Logical indicating whether to ask user to check the format of the `sample_id` argument. Defaults to `TRUE`.
`run_chr_size_bias`	Logical indicating whether to run the chromosome size bias analysis. All included analysis can be turned off in this way. Defaults to `TRUE`.
`run_centromeres`	Logical indicating whether to run the signal at centromere analysis. Defaults to `TRUE`.
`run_rDNA`	Logical indicating whether to run the signal flanking rDNA analysis. Defaults to `TRUE`.
`run_telomeres`	Logical indicating whether to run the signal at sub-telomeric region analysis. Defaults to `TRUE`.
`run_dsb_hotspots`	Logical indicating whether to run the signal at DSB hotspot analysis. Defaults to `TRUE`.
`run_axis`	Logical indicating whether to run the signal at axis binding site analysis. Defaults to `TRUE`.
`run_meta_orf`	Logical indicating whether to run the meta ORF analysis. Defaults to `TRUE`.

Value

A new folder at the specified location (default is .../LabShare/HTGenomics/Opening_act/) containing output plots (as .pdf files) of the included of the following analyses:

Chromosome size bias
Signal at centromeres
Signal flanking rDNA
Signal at sub-telomeric regions
Signal at DSB hotspots
Signal at axis binding sites
Signal at meta ORF

Examples

## Not run: 
opening_act2(signal_data=WT, genome="sacCer3", genotype="WT",
             chip_target="Red1", sample_id="AH119C-040114-sacCer3-2mis")

opening_act2(set1_wiggle, genome="sacCer3", "set1", "Red1",
             "AH8584b-16032016-sacCer3-2mis")

opening_act2(rec8, genome="SK1Yue", "rec8", "Red1",
             "AH8115b-24042015-SK1Yue-PM", user_input=FALSE,
             run_meta_orf=FALSE)
            
opening_act2(signal_data=WT, genome="sacCer3", genotype="WT",
             chip_target="Red1", sample_id="AH119C-040114-sacCer3-2mis",
             run_meta_orf=FALSE)

opening_act2(signal_data=WT, genome="sacCer3", genotype="dot1",
             chip_target="Red1", sample_id="AH8104-010116-sacCer3-2mis",
             output_path='~/Desktop',
             run_chr_size_bias=FALSE, run_centromeres=FALSE, run_rDNA=FALSE,
             run_telomeres=FALSE, run_dsb_hotspots=TRUE, run_axis=TRUE,
             run_meta_orf=FALSE)

## End(Not run)

hochwagenlab/hwglabr2 documentation built on Nov. 12, 2022, 7:27 p.m.