pre_process: Pre-process methylation array data from (raw) .idat files to...

In ijcBIT/cnv.methyl: cnv.methyl finds copy number alteration from methylation idat files

Pre-process methylation array data from (raw) .idat files to segment & log2r intensity files calculated by CONUMEE.

Description

construct RGChannelSet in parallel using foreach

Generate Qc reports

Usage

pre_process(
  targets,
  purity = NULL,
  query = T,
  RGset = T,
  out = "./analysis/intermediate/",
  idats_folder = NULL,
  subf = "IDATS/",
  folder = NULL,
  ncores = NULL,
  arraytype = NULL,
  copy = FALSE,
  frac = 0.1,
  pval = 0.01,
  remove_sex = TRUE,
  sampGroups = NULL
)

pre_process.myLoad(
  targets,
  folder,
  arraytype = "450K",
  ncores = NULL,
  files = NULL,
  copy = FALSE
)

qc(
  rgSet,
  sampGroups = NULL,
  sampNames = "Sample_Name",
  qc_folder = "analysis/intermediate/QC/"
)

purify(myLoad, knn = 5)

queryfy(
  targets,
  rgSet,
  sampGroups = NULL,
  sampNames = "Sample_Name",
  frac = 0.1,
  pval = 0.01,
  remove_sex = TRUE,
  arraytype = NULL,
  qc_folder = "analysis/intermediate/QC"
)

Arguments

targets	A sample sheet with the required fields for ChAMP to load files.
purity	Whether or not you want purity imputed by Rfpurify. Default=TRUE.
query	Set to TRUE when you are only interested in imputing purity. Default=TRUE
RGset	Whether you want normalised "RGChannelSet" or "RGChannelSetExtended" to be saved or not. path=out
out	Results folder to store the normalized and clean RGset.
idats_folder	Folder containing idats. It will try to guess which idat belongs to which row in the targets data.frame.
subf	Subfolder inside results folder where IDAT files will be copied.
folder	this directory will be created as the combination of out and subf. if you save the csv file inside this folder it will be used by minfi::read.450k.sheet.
ncores	number of cores to use.
arraytype	Methylation array type
copy	Change to TRUE if you want to copy files to idats folder. Useful when working in HPC and idats are in ISILON.
frac	Fraction of faulty probes (P-value > pval ) allowed. default 0.1
pval	P-value cutoff. default 0.01
remove_sex	Boolean. Should sex chromosomes be removed? default = TRUE
sampGroups	Groups for qc report & plots color category.
files	Files
rgSet	Input RGChannelSet object with raw idats and metadata.
sampNames	Sample names to be used for labels.
qc_folder	Path to location where qc_report and plot will be saved.
myLoad	a RGset as returned by minfi::read.metharray.exp. will use this as basedir to load the idats. default is results/IDATS/.
knn	number of neighbors for knn algorithm

Value

Log2r intensities ready to be analysed with conumee.

RGset

Qc plots

Normalized & filtered RGset.

Author(s)

izar de Villasante

izar de Villasante

Examples

data("TrainingSet_Sample_sheet")
ss<-TrainingSet_Sample_sheet[1:56,]
pre_process(ss)

ijcBIT/cnv.methyl documentation built on Jan. 10, 2023, 7:51 a.m.