BaalChIP-class

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Description

This S4 class includes a series of methods for detecting allele-specific events from multiple ChIP-seq datasets.

Usage

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BaalChIP(samplesheet = NULL, hets = NULL, CorrectWithgDNA = list())

Arguments

samplesheet

A character string indicating the filename for a .tsv file. Column names in the .tsv file should include:

  • group_name: identifier string to group samples together

  • target: identifier string for factor (transcription factor, protein)

  • replicate_number: replicate number of sample

  • bam_name: file path for BAM file containing aligned reads for ChIP sample. If duplicated reads are flaged they will not be included in the allelic count data

  • bed_name: path for BED file containing peaks for ChIP sample

  • SampleID: identifier string for sample. If not given will use <group_name>_<target>_<replicate_number>

hets

A named vector with filenames for the .txt variant files to be used. The names in the vector should correspond to group_name strings in the .tsv samplesheet. Columns names in the .txt file should include:

  • ID: unique identifier string per variant. Identifiers have to be unique, and no more than one identifier should be present per data record. If there is no identifier available, then use an arbritary name to name each variant

  • CHROM: chromosome identifier from the reference genome per variant (same genome build as BAM and BED files provided)

  • POS: the reference position (1-based)

  • REF: reference base. Each base must be one of A,C,G,T in uppercase. Multiple bases are not permitted

  • ALT: alternate non-reference base. Each base must be one of A,C,G,T in uppercase. Multiple bases are not permitted

  • RAF: [Optional] a value ranging from 0 to 1 for each variant denoting the relative allele frequency (RAF). A value between 0.5 and 1 denotes a bias to the reference allele, and a value between 0 and 0.5 a bias to the alternate allele. If neither RAF or CorrectWithgDNA are given, BaalChIP will not correct for relative allele frequency (copy-number) bias. If both RAF and CorrectWithgDNA are given, BaalChIP will give priority to the RAF values of the 'hets' files and will use these values to correct for relative allele frequency (copy-number) bias.

CorrectWithgDNA

An optional named list with comple file paths for the .bam gDNA files to be used. The names in the list should correspond to group_name strings in the .tsv samplesheet. Allelic read counts from all gDNA files are pooled together to generate the Reference Allelic Ratios (RAF) directly from input data. If missing, BaalChIP will try to read the background allelic ratios from the information in the RAF column of the 'hets' files indicated by the hets parameter. If both RAF and CorrectWithgDNA are missing, BaalChIP will not correct for relative allele frequency (copy-number) bias.

Value

.Object An object of the BaalChIP class.

Author(s)

Ines de Santiago, Wei Liu, Ke Yuan, Florian Markowetz

Examples

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setwd(system.file("test",package="BaalChIP"))
samplesheet <- "exampleChIP.tsv"
hets <- c("MCF7"="MCF7_hetSNP.txt", "GM12891"="GM12891_hetSNP.txt")
res <- new("BaalChIP", samplesheet=samplesheet, hets=hets)
res <- BaalChIP(samplesheet=samplesheet, hets=hets)