run_conumee: Generate segment & log2r intensity files calculated by...

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

Generate segment & log2r intensity files calculated by CONUMEE.

Description

Generate segment & log2r intensity files calculated by CONUMEE.

read intesity from file or object

Usage

run_conumee(
  intensities,
  anno_file = NULL,
  ctrl_file = "WB",
  Sample_Name = NULL,
  seg.folder = "Segments",
  log2r.folder = "log2r",
  arraytype = "450K",
  conumee.folder = "analysis/CONUMEE/",
  probeid = "probeid"
)

read_intensity(infile, Sample_Name = NULL, probeid = "probeid")

Arguments

intensities	dataset with intensities. either dataframe or path to file. For big datasets '.fst' file is recomended.
anno_file	anno file CNV.anno object saved as .rds. default CNV_Germline_GSITIC2_BROAD_SNP6.merged.151117.hg19.CNV.txt
ctrl_file	CNV data object with intensities from the controls group. must be compressed as '.rds' file format, default uses 96 WB samples. Default='WB'
Sample_Name	Samples to be analysed. If is NULL all columns in input file will be used. Accepts numbered index and names. Default=NULL
seg.folder	Subfolder inside results where segment files are saved. The segments are generated with CONUMEE CNV.segment(CNV.detail(CNV.bin(fit))) default = "Segments"
log2r.folder	Subfolder inside results where log2r values are saved. log2r values are the log2 ratio of the intensities(_GRN + _RED channel) between the query and the reference set (control) as returned by CNV.fit function from CONUMEE. default = "log2r"
arraytype	Methylation array type
conumee.folder	Parent working directory where you want to have your results.
probeid	name of column with probe ids.
infile	input path to file or object

Value

Log2r intensities and segment files.

Examples

#data("anno")
#data("controls")
#library(conumee)
library(SummarizedExperiment)
intensity<-readRDS("./analysis/ChAMP/intensities.rds")
intensity<-conumee::CNV.load(intensity)@intensity
run_conumee(intensities=intensity)

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