qc_idats: Compute quality-control of methylation array from Illumina...
In omicsr/dmapaq: DNA Methylation Arrays Processing And Quality-Control

Description Usage Arguments

View source: R/qc_idats.R

Compute quality-control of methylation array from Illumina using a rmarkdown template.

qc_idats(
  csv_file,
  data_directory,
  array = "EPIC",
  annotation = "ilm10b4.hg19",
  cohort_name = "COHORT",
  output_file = paste(cohort_name, array, "QC.html", sep = "_"),
  output_directory = ".",
  filter_snps = TRUE,
  filter_non_cpg = TRUE,
  filter_xy = TRUE,
  filter_multihit = TRUE,
  filter_beads = TRUE,
  population = NULL,
  bead_cutoff = 0.05,
  detection_pvalues = 0.01,
  filter_callrate = TRUE,
  callrate_samples = 0.99,
  callrate_probes = 1,
  gender_threshold = -2,
  gender_colname = NULL,
  norm_background = "oob",
  norm_dye = "RELIC",
  norm_quantile = "quantile1",
  cell_tissue = NULL,
  pca = TRUE,
  pca_vars = c("Sample_Plate", "Sentrix_ID"),
  pca_threshold = 2,
  max_labels = 15,
  title = paste(array, "Array Quality-Control"),
  author_name = "Unknown",
  author_affiliation = NULL,
  author_email = NULL,
  encoding = "UTF-8",
  ...
)

`csv_file`	A `character`. The path to a CSV file, i.e., a sample sheet describing the data.
`data_directory`	A `character`. The path to the data directory.
`array`	A `character`. The array name, i.e., `"EPIC"` or `"450k"`.
`annotation`	A `character`. The name and version of the annotation package to be used.
`cohort_name`	A `character`. The name of the studied cohort / population.
`output_file`	A `character`. The name of the html file produced.
`output_directory`	A `character`. The path to the output directory.
`filter_snps`	A `logical`. Should the probes in which the probed CpG falls near a SNP (according to (Zhou et al., 2016)) be removed? Default is `TRUE`.
`filter_non_cpg`	A `logical`. Should the non-cg probes be removed?
`filter_xy`	A `logical`. Should the probes from X and Y chromosomes be removed? Default is `TRUE`.
`filter_multihit`	A `logical`. Should the probes which align to multiple locations (according to Nordlund et al., 2013) be removed? Default is `TRUE`.
`filter_beads`	A `logical`. Should the probes with a beadcount less than 3 be removed? Default is `TRUE`.
`population`	A `character`. Name of the ethnicity population to be used. Default is `NULL` for none.
`bead_cutoff`	A `numeric`. The threshold for beadcount. Default is `0.05`.
`detection_pvalues`	A `numeric`. The threshold for the detection pvalues above which, values are considered as missing. Default is `0.01`.
`filter_callrate`	A `logical`. Should the data be filtered based on call rate metric? Default is `TRUE`.
`callrate_samples`	A `numeric`. The call rate threshold for samples, under which samples are excluded. Default is `0.99`.
`callrate_probes`	A `numeric`. The call rate threshold for probes, under which probes are excluded. Default is `1`.
`gender_threshold`	A `numeric`. The threshold value to discrimate gender based on sexual chromosomes methylation. Default is `-2`.
`gender_colname`	A `character`. The name of the column containing the gender in the file provided in `csv_file`. Default is `NULL`.
`norm_background`	A `character`. Optional method to estimate background normal distribution parameters. This must be one of `"oob"`, `"est"` or `"neg"`. Default is `"oob"`.
`norm_dye`	A `character`. Dye bias correction, "mean": correction based on averaged red/green ratio; or `"RELIC"`: correction with RELIC method; or `"none"`: no dye bias correction. Default is `"RELIC"`.
`norm_quantile`	A `character`. The quantile normalisation to be used. This should be one of `"quantile1"`, `"quantile2"`, or `"quantile3"`. Default is `"quantile1"`.
`cell_tissue`	A `character`. The cell tissue to be used for cell composition estimation, using a reference panel (i.e., `"blood"` or `"cordblood"`) or a mathematical deconvolution. Default is `NULL`.
`pca`	A `logical`. Whether or not a PCA should be performed on the dataset. Default is `TRUE`.
`pca_vars`	A `vector(character)`. Variables to be used with factorial planes. Default is `c("Sample_Plate", "Sentrix_ID")`.
`pca_threshold`	A `numeric`. The number of times the interquartile range from the upper and lower quartile at which sa sample is defined as an outlier. Default is `2`.
`max_labels`	A `numeric`. The maximum number of labels to show on plots. Default is `15`
`title`	A `character`. The report's title. Default is `paste(array, "Array Quality-Control")`.
`author_name`	A `character`. The author's name to be printed in the report. Default is `Unknown`.
`author_affiliation`	A `character`. The affiliation to be printed in the report. Default is `NULL`.
`author_email`	A `character`. The email to be printed in the report. Default is `NULL`.
`encoding`	A `character`. The encoding to be used for the html report. Default is `"UTF-8"`.
`...`	Parameters to pass to `rmarkdown::render()`.