get_differential_methylation.Rdget_differential_methylation
get_differential_methylation(
patient_id,
sample_id,
sex,
normal_origin_proxy_id,
path,
path_to_CAMDAC,
build,
effect_size = 0.2,
prob = 0.99,
min_DMP_counts_in_DMR = 5,
min_consec_DMP_in_DMR = 4,
n_cores,
reseg = FALSE,
bulk = FALSE
)Character variable containting the patient id number
Character variable with the tumour sample_id
Character variable with the patient expressed as "XX" for female or "XY" for male.
Character variable with the sample ID of the normal to be used as a proxy for the tumour cell of origin in
Character path variable pointing to the desired working directory. This is where the output will be stored.
Character variable containting the path to the CAMDAC directory including dir name (e.g. "/path/to/CAMDAC/").
Character variable corresponding to the reference genome used for alignment. CAMDAC is compatible with "hg19", "hg38", "GRCH37","GRCH38".
Numerical containting the minimum tumour-normal methylation difference (default is 0.2)
Numerical value representing the threshold for statistically significant DMP (default is p=0.99)
Numerical value representing the number of DMPs required in a DMR
Numerical value representing the number of consecutive DMPs required in a DMR
Numerical value correspdonding to the number of cores for parallel processing
Logical value should be set to FALSE. Multi-sample re-segmentation of the copy number profiles will be available in future versions of CAMDAC.
Default is FALSE unless you want bulk DMP/DMR calls in addition to CAMDAC pure tumour differential methylation analysis
Note: #' Annotation include: CGI (including shore and shelves) gene body (intragenic, 5UTR, 3UTR, intron, exon) promoter (2kb upstream and 500 downstream any UCSC annotated gene) enhancer (vista and FANTOM5 annotation)
Biologically significant DMPs, DMRs