Standard analysis of ChIP-seq experiments

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/.

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:

  1. "SK1Yue"

  2. "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:

  1. Chromosome size bias

  2. Signal at centromeres

  3. Signal flanking rDNA

  4. Signal at sub-telomeric regions

  5. Signal at DSB hotspots

  6. Signal at axis binding sites

  7. 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)
# }