spikein_normalization_factor: Compute spike-in normalization factor

In hochwagenlab/hwglabr2: Collection of R functions used in the Hochwagen Lab

Compute spike-in normalization factor

Description

Computes spike-in normalization factor between two spiked-in samples. Inputs text files containing counts of aligned reads per chromosome of a hybrid SK1:S288C genome.

Usage

spikein_normalization_factor(
  ref_chip_counts,
  ref_input_counts,
  test_chip_counts,
  test_input_counts
)

Arguments

ref_chip_counts	Either a single or a list of paths to reference ChIP samples' read counts file. No default.
ref_input_counts	Either a single or a list of paths to reference input samples' read counts file. No default.
test_chip_counts	Either a single or a list of paths to test ChIP samples' read counts file. No default.
test_input_counts	Either a single or a list of paths to test input samples' read counts file. No default.

Value

Numeric normalization factor.

Examples

## Not run: 
spikein_normalization_factor(ref_chip_counts='Counts_AH119_chip.txt',
                             ref_input_counts='Counts_AH119_input.txt',
                             test_chip_counts='Counts_AH8104_chip.txt',
                             test_input_counts='Counts_AH8104_input.txt')

spikein_normalization_factor(ref_chip_counts=list('Counts_AH119_chip_1.txt',
                                                  'Counts_AH119_chip_2.txt',
                                                  'Counts_AH119_chip_3.txt'),
                             ref_input_counts=list('Counts_AH119_inp_1.txt',
                                                   'Counts_AH119_inp_2.txt',
                                                   'Counts_AH119_inp_3.txt'),
                             test_chip_counts='Counts_AH8104_chip.txt',
                             test_input_counts='Counts_AH8104_input.txt')

## End(Not run)

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