candidate/coProject.R
In jokergoo/cotools: R functions
cp = setRefClass("coProject",
fields = list(
sample_id = "character",
type = "character",
col = "character",
chromosome = "character",
species = "character",
txdb = "ANY",
methylation_hooks = "ANY",
WGBS = "ANY",
expr = "ANY",
RNASEQ = "ANY",
genomic_features = "ANY",
CHIPSEQ = "ANY",
get_hm = "ANY",
output = "list"
)
)
initialize_project = function(sample_id, chromosome, species,
type, col, output,
chipseq,
txdb,
methylation_hooks, expr,
get_hm,
genomic_features, dir = ".", gencode_gtf_file = NULL) {
cp = new("coProject")
if(missing(sample_id)) {
stop("'sample_id' is mandatory.")
}
cp$sample_id = sample_id
if(!missing(type)) {
if(length(type) != length(sample_id)) {
stop("'type' should have same length as 'sample_id'.")
}
cp$type = type
}
if(!missing(col)) {
if(is.numeric(col)) col = rgb(t(col2rgb(col)), maxColorValue = 255)
if(!missing(type)) {
if(!is.null(names(col)) && length(col) == length(unique(type))) {
cp$col = col
} else if(length(col) == length(sample_id)) {
cp$col = structure(unique(col), names = unique(type))
} else {
stop("'col' should have same length as 'sample_id', or a named vector corresponding to 'type'.")
}
} else {
stop("You should define 'type' if you want to define 'col'.")
}
}
if(missing(chromosome)) {
stop("'chromosome' must be defined.")
}
cp$chromosome = as.character(chromosome)
if(missing(species)) {
stop("'species' must be defined.")
}
cp$species = species
if(!missing(txdb)) {
cp$txdb = txdb
}
if(!missing(methylation_hooks)) {
if(!inherits(methylation_hooks, "GlobalOptionsFun")) {
stop("You should use 'GlobalOptions::setGlobalOptions' to generate 'methylation_hooks'.")
}
cat("validate methylation (random pick one chromosome)...\n")
methylation_hooks$set(sample(chromosome, 1))
cn = intersect(colnames(methylation_hooks$meth(row_index = 1:2)), sample_id)
if(length(cn) == 0) {
stop("samples names for methylation should correspond to 'sample_id'.")
}
methylation_hooks$raw(row_index = 1, col_index = 1)
methylation_hooks$coverage(row_index = 1, col_index = 1)
methylation_hooks$site(index = 1)
methylation_hooks$GRanges()
cp$methylation_hooks = methylation_hooks
cp$WGBS = sample_id %in% cn
}
if(!missing(expr)) {
if(is.data.frame(expr)) {
stop("I don't like expression stored in a data frame, change to matrix.")
}
cat("validate expression...\n")
cn = intersect(sample_id, colnames(expr))
if(length(cn) == 0) {
stop("column names of 'expr' should correspond to 'sample_id'.")
}
expr = expr[, cn, drop = FALSE]
# test row names in 'expr' and names in 'txdb'
if(!missing(txdb)) {
genes = genes(txdb)
gn = intersect(names(genes), rownames(expr))
if(length(gn) == 0) {
stop("row names of 'expr' should correspond to 'txdb'.")
}
}
cp$expr = expr
cp$RNASEQ = sample_id %in% cn
}
if(!missing(genomic_features)) {
if(!all(sapply(genomic_features, inherits, "GRanges"))) {
stop("'genomic_features' should be a list of 'GRanges' objects.")
}
if(is.null(names(genomic_features))) {
stop("'genomic_features' should be a named list.")
}
cp$genomic_features = genomic_features
}
if(!missing(chipseq)) {
cat("validate chipseq (random pick one sample)...\n")
histome_marks = names(chipseq)
if(is.null(histome_marks)) {
stop("'chipseq' should be a list with names of histome marks.")
}
lt = lapply(seq_along(chipseq), function(i) {
cn = intersect(chipseq[[i]], sample_id)
if(length(cn) == 0) {
stop(qq("sample ids for '@{histome_marks[i]}' should correspond to 'sample_id'."))
}
sample_id %in% cn
})
names(lt) = histome_marks
cp$CHIPSEQ = lt
if(missing(get_hm)) {
stop("since you specified 'chipseq', 'get_hm' should be defined as well.")
}
# test get_hm
lapply(seq_along(lt), function(i) {
gr = get_hm(sample_id[lt[[i]]][1], histome_marks[i])
if(!inherits(gr, "GRanges")) {
stop("'get_hm' should return a 'GRanges' object.")
}
if(is.null(gr$density)) {
stop("the 'Granges' object should contain a column 'density'.")
}
})
cp$get_hm = get_hm
}
## initialize output folder structure
dir.create(dir, showWarnings = FALSE, recursive = TRUE)
dir.create(qq("@{dir}/rds/"), showWarnings = FALSE, recursive = TRUE)
dir.create(qq("@{dir}/image/"), showWarnings = FALSE, recursive = TRUE)
dir.create(qq("@{dir}/temp/"), showWarnings = FALSE, recursive = TRUE)
dir.create(qq("@{dir}/table/"), showWarnings = FALSE, recursive = TRUE)
if(!missing(output)) {
cp$output = list(base = dir,
rds = qq("@{dir}/rds/"),
image = qq("@{dir}/image/"),
temp = qq("@{dir}/temp/"),
table = qq("@{dir}/table/"))
}
return(cp)
}
cp$methods(
show = function() {
qqcat(
"Summary of the coProject:
| samples: @{length(.self$sample_id)}
| chromosomes: @{length(.self$chromosome)}
| species: @{.self$species}
")
if(!is.null(.self$type)) {
qqcat("| types: @{length(unique(.self$type))}\n")
}
if(!is.null(.self$txdb)) {
qqcat("| txdb: @{.self$txdb@.xData$conn@dbname}\n")
}
if(!is.null(.self$WGBS)) {
qqcat("| WGBS: @{sum(.self$WGBS)}\n")
}
if(!is.null(.self$RNASEQ)) {
qqcat("| RNASEQ: @{sum(.self$RNASEQ)}\n")
}
if(!is.null(.self$CHIPSEQ)) {
histome_marks = names(.self$CHIPSEQ)
qqcat("| CHIPSEQ:\n")
for(hm in histome_marks) {
qqcat("| @{hm}: @{sum(.self$CHIPSEQ[[hm]])}\n")
}
}
if(!is.null(.self$genomic_features)) {
qqcat("| genomic features:\n")
gf = names(.self$genomic_features)
for(i in seq_along(.self$genomic_features)) {
qqcat("| @{gf[i]}: @{length(.self$genomic_features[[i]])}\n")
}
}
if(length(.self$output) > 0) {
qqcat("| output: @{.self$output$base}\n")
}
qqcat("\nYou can save this object to get rid of spending a lot of time to re-create it.\n\n")
},
correlated_regions = function(sample_id, chr, ...) {
l = rep(TRUE, length(.self$sample_id))
if(!missing(sample_id)) {
l = .self$sample_id %in% sample_id
}
l = l & .self$WGBS & .self$RNASEQ
sample_id = .self$sample_id[l]
cat("samples that both have WGBS and RNASEQ:", sum(l), "\n")
if(is.null(.self$type)) {
factor = NULL
} else {
factor = .self$type[l]
}
methylation_hooks = .self$methylation_hooks
e = environment()
parent.env(parent.env(e))$correlated_regions(sample_id,
expr = .self$expr[, sample_id, drop = FALSE],
txdb = .self$txdb,
chr = chr,
factor = factor,
...)
},
filter_correlated_regions = function(template, chromosome = .self$chromosome, ...) {
methylation_hooks = .self$methylation_hooks
e = environment()
parent.env(parent.env(e))$filter_correlated_regions(chromosome = chromosome, template = template, ...)
},
reduce_cr = function(cr, ...) {
methylation_hooks = .self$methylation_hooks
e = environment()
parent.env(parent.env(e))$reduce_cr(cr = cr, expr = .self$expr, txdb = .self$txdb, ...)
},
cr_qc = function(template, chromosome = .self$chromosome) {
methylation_hooks = .self$methylation_hooks
e = environment()
parent.env(parent.env(e))$cr_qc(chromosome = chromosome, template = template)
},
cr_correlated_to_genomic_features = function(cr) {
methylation_hooks = .self$methylation_hooks
e = environment()
parent.env(parent.env(e))$cr_correlated_to_genomic_features(cr, gf_list = .self$genomic_features, species = .self$species)
},
cr_hilbert = function(cr, template, chromosome = .self$chromosome) {
methylation_hooks = .self$methylation_hooks
e = environment()
parent.env(parent.env(e))$cr_hilbert(cr, template, txdb = .self$txdb, chromosome = chromosome)
},
compare_meth = function(chr, start, end, x = NULL, x2 = NULL) {
methylation_hooks = .self$methylation_hooks
e = environment()
parent.env(parent.env(e))$compare_meth(chr, start, end, x, x2)
},
cr_gviz = function(cr, gi, gf_list = NULL, ...) {
methylation_hooks = .self$methylation_hooks
e = environment()
parent.env(parent.env(e))$cr_gviz(cr, gi, expr = .self$expr, txdb = .self$txdb,
species = .self$species, gf_list = .self$genomic_features[gf_list])
},
cr_scatterplot_me = function(cr, gi = NULL, ...) {
methylation_hooks = .self$methylation_hooks
e = environment()
parent.env(parent.env(e))$cr_scatterplot_me(cr, expr = .self$expr,
gi = gi, annotation_color = .self$col)
},
cr_enriched_at_tss = function(cr) {
methylation_hooks = .self$methylation_hooks
e = environment()
parent.env(parent.env(e))$cr_enriched_at_tss(cr, .self$txdb)
},
enriched_heatmap_list_on_gene = function(cr, cgi, hm_name = NULL, on = "tss", by = "gene", ...) {
methylation_hooks = .self$methylation_hooks
e = environment()
if(is.null(.self$CHIPSEQ) || is.null(hm_name)) {
parent.env(parent.env(e))$enriched_heatmap_list_on_gene(cr, cgi, txdb = .self$txdb, expr = .self$expr, on = no, by = by, ...)
} else {
sid = .self$sample_id[.self$CHIPSEQ[[hm_name]]]
hm_list = lapply(sid, function(x) .self$get_hm(hm_name, x))
names(hm_list) = sid
parent.env(parent.env(e))$enriched_heatmap_list_on_gene(cr, cgi, txdb = .self$txdb, expr = .self$expr, hm_list = hm_list, hm_name = hm_name, on = no, by = by, ...)
}
},
enriched_heatmap_list_on_tss_cgi = function(cr, cgi, hm_name = NULL, by = "gene", ...) {
methylation_hooks = .self$methylation_hooks
e = environment()
if(is.null(.self$CHIPSEQ) || is.null(hm_name)) {
parent.env(parent.env(e))$enriched_heatmap_list_on_tss_cgi(cr, cgi, txdb = .self$txdb, expr = .self$expr, by = by, ...)
} else {
sid = .self$sample_id[.self$CHIPSEQ[[hm_name]]]
hm_list = lapply(sid, function(x) .self$get_hm(hm_name, x))
names(hm_list) = sid
parent.env(parent.env(e))$enriched_heatmap_list_on_tss_cgi(cr, cgi, txdb = .self$txdb, expr = .self$expr, hm_list = hm_list, hm_name = hm_name, by = by, ...)
}
},
wgbs_qcplot = function(sample_id, chromosome = .self$chromosome) {
methylation_hooks = .self$methylation_hooks
e = environment()
parent.env(parent.env(e))$wgbs_qcplot(sample_id, chromosome)
},
plot_coverage_and_methylation_on_genome = function(sid, chromosome = .self$chromosome, nw = 10000, ...) {
methylation_hooks = .self$methylation_hooks
e = environment()
parent.env(parent.env(e))$plot_coverage_and_methylation_on_genome(sid, chromosome, .self$species, nw, ...)
},
plot_multiple_samples_methylation_on_genome = function(sample_id, chromosome = .self$chromosome, nw = 1000, ...) {
methylation_hooks = .self$methylation_hooks
e = environment()
parent.env(parent.env(e))$plot_multiple_samples_methylation_on_genome(sample_id, annotation = .self$type,
annotation_color = chromosome, species = .self$species, nw = nw, ...)
},
global_methylation_distribution = function(sample_id, chromosome = .self$chromosome, by_chr = FALSE) {
methylation_hooks = .self$methylation_hooks
e = environment()
parent.env(parent.env(e))$global_methylation_distribution(sample_id, annotation = .self$type,
annotation_color = .self$col, chromosome = chromosome, by_chr = by_chr)
},
get_mean_methylation_in_genomic_features = function(sample_id, chromosome = .self$chromosome, gf_list = NULL) {
methylation_hooks = .self$methylation_hooks
e = environment()
parent.env(parent.env(e))$get_mean_methylation_in_genomic_features(sample_id, gf_list = .self$genomic_features[gf_list],
chromosome = chromosome)
},
heatmap_diff_methylation_in_genomic_features = function(gr, ...) {
methylation_hooks = .self$methylation_hooks
e = environment()
parent.env(parent.env(e))$heatmap_diff_methylation_in_genomic_features(gr, annotation = .self$type,
annotation_color = .self$col, txdb = .self$txdb, gf_list = .self$genomic_features, ...)
},
pipeline = function() {
}
)
jokergoo/cotools documentation built on May 19, 2019, 6:24 p.m.
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cp = setRefClass("coProject",
fields = list(
sample_id = "character",
type = "character",
col = "character",
chromosome = "character",
species = "character",
txdb = "ANY",
methylation_hooks = "ANY",
WGBS = "ANY",
expr = "ANY",
RNASEQ = "ANY",
genomic_features = "ANY",
CHIPSEQ = "ANY",
get_hm = "ANY",
output = "list"
)
)
initialize_project = function(sample_id, chromosome, species,
type, col, output,
chipseq,
txdb,
methylation_hooks, expr,
get_hm,
genomic_features, dir = ".", gencode_gtf_file = NULL) {
cp = new("coProject")
if(missing(sample_id)) {
stop("'sample_id' is mandatory.")
}
cp$sample_id = sample_id
if(!missing(type)) {
if(length(type) != length(sample_id)) {
stop("'type' should have same length as 'sample_id'.")
}
cp$type = type
}
if(!missing(col)) {
if(is.numeric(col)) col = rgb(t(col2rgb(col)), maxColorValue = 255)
if(!missing(type)) {
if(!is.null(names(col)) && length(col) == length(unique(type))) {
cp$col = col
} else if(length(col) == length(sample_id)) {
cp$col = structure(unique(col), names = unique(type))
} else {
stop("'col' should have same length as 'sample_id', or a named vector corresponding to 'type'.")
}
} else {
stop("You should define 'type' if you want to define 'col'.")
}
}
if(missing(chromosome)) {
stop("'chromosome' must be defined.")
}
cp$chromosome = as.character(chromosome)
if(missing(species)) {
stop("'species' must be defined.")
}
cp$species = species
if(!missing(txdb)) {
cp$txdb = txdb
}
if(!missing(methylation_hooks)) {
if(!inherits(methylation_hooks, "GlobalOptionsFun")) {
stop("You should use 'GlobalOptions::setGlobalOptions' to generate 'methylation_hooks'.")
}
cat("validate methylation (random pick one chromosome)...\n")
methylation_hooks$set(sample(chromosome, 1))
cn = intersect(colnames(methylation_hooks$meth(row_index = 1:2)), sample_id)
if(length(cn) == 0) {
stop("samples names for methylation should correspond to 'sample_id'.")
}
methylation_hooks$raw(row_index = 1, col_index = 1)
methylation_hooks$coverage(row_index = 1, col_index = 1)
methylation_hooks$site(index = 1)
methylation_hooks$GRanges()
cp$methylation_hooks = methylation_hooks
cp$WGBS = sample_id %in% cn
}
if(!missing(expr)) {
if(is.data.frame(expr)) {
stop("I don't like expression stored in a data frame, change to matrix.")
}
cat("validate expression...\n")
cn = intersect(sample_id, colnames(expr))
if(length(cn) == 0) {
stop("column names of 'expr' should correspond to 'sample_id'.")
}
expr = expr[, cn, drop = FALSE]
# test row names in 'expr' and names in 'txdb'
if(!missing(txdb)) {
genes = genes(txdb)
gn = intersect(names(genes), rownames(expr))
if(length(gn) == 0) {
stop("row names of 'expr' should correspond to 'txdb'.")
}
}
cp$expr = expr
cp$RNASEQ = sample_id %in% cn
}
if(!missing(genomic_features)) {
if(!all(sapply(genomic_features, inherits, "GRanges"))) {
stop("'genomic_features' should be a list of 'GRanges' objects.")
}
if(is.null(names(genomic_features))) {
stop("'genomic_features' should be a named list.")
}
cp$genomic_features = genomic_features
}
if(!missing(chipseq)) {
cat("validate chipseq (random pick one sample)...\n")
histome_marks = names(chipseq)
if(is.null(histome_marks)) {
stop("'chipseq' should be a list with names of histome marks.")
}
lt = lapply(seq_along(chipseq), function(i) {
cn = intersect(chipseq[[i]], sample_id)
if(length(cn) == 0) {
stop(qq("sample ids for '@{histome_marks[i]}' should correspond to 'sample_id'."))
}
sample_id %in% cn
})
names(lt) = histome_marks
cp$CHIPSEQ = lt
if(missing(get_hm)) {
stop("since you specified 'chipseq', 'get_hm' should be defined as well.")
}
# test get_hm
lapply(seq_along(lt), function(i) {
gr = get_hm(sample_id[lt[[i]]][1], histome_marks[i])
if(!inherits(gr, "GRanges")) {
stop("'get_hm' should return a 'GRanges' object.")
}
if(is.null(gr$density)) {
stop("the 'Granges' object should contain a column 'density'.")
}
})
cp$get_hm = get_hm
}
## initialize output folder structure
dir.create(dir, showWarnings = FALSE, recursive = TRUE)
dir.create(qq("@{dir}/rds/"), showWarnings = FALSE, recursive = TRUE)
dir.create(qq("@{dir}/image/"), showWarnings = FALSE, recursive = TRUE)
dir.create(qq("@{dir}/temp/"), showWarnings = FALSE, recursive = TRUE)
dir.create(qq("@{dir}/table/"), showWarnings = FALSE, recursive = TRUE)
if(!missing(output)) {
cp$output = list(base = dir,
rds = qq("@{dir}/rds/"),
image = qq("@{dir}/image/"),
temp = qq("@{dir}/temp/"),
table = qq("@{dir}/table/"))
}
return(cp)
}
cp$methods(
show = function() {
qqcat(
"Summary of the coProject:
| samples: @{length(.self$sample_id)}
| chromosomes: @{length(.self$chromosome)}
| species: @{.self$species}
")
if(!is.null(.self$type)) {
qqcat("| types: @{length(unique(.self$type))}\n")
}
if(!is.null(.self$txdb)) {
qqcat("| txdb: @{.self$txdb@.xData$conn@dbname}\n")
}
if(!is.null(.self$WGBS)) {
qqcat("| WGBS: @{sum(.self$WGBS)}\n")
}
if(!is.null(.self$RNASEQ)) {
qqcat("| RNASEQ: @{sum(.self$RNASEQ)}\n")
}
if(!is.null(.self$CHIPSEQ)) {
histome_marks = names(.self$CHIPSEQ)
qqcat("| CHIPSEQ:\n")
for(hm in histome_marks) {
qqcat("| @{hm}: @{sum(.self$CHIPSEQ[[hm]])}\n")
}
}
if(!is.null(.self$genomic_features)) {
qqcat("| genomic features:\n")
gf = names(.self$genomic_features)
for(i in seq_along(.self$genomic_features)) {
qqcat("| @{gf[i]}: @{length(.self$genomic_features[[i]])}\n")
}
}
if(length(.self$output) > 0) {
qqcat("| output: @{.self$output$base}\n")
}
qqcat("\nYou can save this object to get rid of spending a lot of time to re-create it.\n\n")
},
correlated_regions = function(sample_id, chr, ...) {
l = rep(TRUE, length(.self$sample_id))
if(!missing(sample_id)) {
l = .self$sample_id %in% sample_id
}
l = l & .self$WGBS & .self$RNASEQ
sample_id = .self$sample_id[l]
cat("samples that both have WGBS and RNASEQ:", sum(l), "\n")
if(is.null(.self$type)) {
factor = NULL
} else {
factor = .self$type[l]
}
methylation_hooks = .self$methylation_hooks
e = environment()
parent.env(parent.env(e))$correlated_regions(sample_id,
expr = .self$expr[, sample_id, drop = FALSE],
txdb = .self$txdb,
chr = chr,
factor = factor,
...)
},
filter_correlated_regions = function(template, chromosome = .self$chromosome, ...) {
methylation_hooks = .self$methylation_hooks
e = environment()
parent.env(parent.env(e))$filter_correlated_regions(chromosome = chromosome, template = template, ...)
},
reduce_cr = function(cr, ...) {
methylation_hooks = .self$methylation_hooks
e = environment()
parent.env(parent.env(e))$reduce_cr(cr = cr, expr = .self$expr, txdb = .self$txdb, ...)
},
cr_qc = function(template, chromosome = .self$chromosome) {
methylation_hooks = .self$methylation_hooks
e = environment()
parent.env(parent.env(e))$cr_qc(chromosome = chromosome, template = template)
},
cr_correlated_to_genomic_features = function(cr) {
methylation_hooks = .self$methylation_hooks
e = environment()
parent.env(parent.env(e))$cr_correlated_to_genomic_features(cr, gf_list = .self$genomic_features, species = .self$species)
},
cr_hilbert = function(cr, template, chromosome = .self$chromosome) {
methylation_hooks = .self$methylation_hooks
e = environment()
parent.env(parent.env(e))$cr_hilbert(cr, template, txdb = .self$txdb, chromosome = chromosome)
},
compare_meth = function(chr, start, end, x = NULL, x2 = NULL) {
methylation_hooks = .self$methylation_hooks
e = environment()
parent.env(parent.env(e))$compare_meth(chr, start, end, x, x2)
},
cr_gviz = function(cr, gi, gf_list = NULL, ...) {
methylation_hooks = .self$methylation_hooks
e = environment()
parent.env(parent.env(e))$cr_gviz(cr, gi, expr = .self$expr, txdb = .self$txdb,
species = .self$species, gf_list = .self$genomic_features[gf_list])
},
cr_scatterplot_me = function(cr, gi = NULL, ...) {
methylation_hooks = .self$methylation_hooks
e = environment()
parent.env(parent.env(e))$cr_scatterplot_me(cr, expr = .self$expr,
gi = gi, annotation_color = .self$col)
},
cr_enriched_at_tss = function(cr) {
methylation_hooks = .self$methylation_hooks
e = environment()
parent.env(parent.env(e))$cr_enriched_at_tss(cr, .self$txdb)
},
enriched_heatmap_list_on_gene = function(cr, cgi, hm_name = NULL, on = "tss", by = "gene", ...) {
methylation_hooks = .self$methylation_hooks
e = environment()
if(is.null(.self$CHIPSEQ) || is.null(hm_name)) {
parent.env(parent.env(e))$enriched_heatmap_list_on_gene(cr, cgi, txdb = .self$txdb, expr = .self$expr, on = no, by = by, ...)
} else {
sid = .self$sample_id[.self$CHIPSEQ[[hm_name]]]
hm_list = lapply(sid, function(x) .self$get_hm(hm_name, x))
names(hm_list) = sid
parent.env(parent.env(e))$enriched_heatmap_list_on_gene(cr, cgi, txdb = .self$txdb, expr = .self$expr, hm_list = hm_list, hm_name = hm_name, on = no, by = by, ...)
}
},
enriched_heatmap_list_on_tss_cgi = function(cr, cgi, hm_name = NULL, by = "gene", ...) {
methylation_hooks = .self$methylation_hooks
e = environment()
if(is.null(.self$CHIPSEQ) || is.null(hm_name)) {
parent.env(parent.env(e))$enriched_heatmap_list_on_tss_cgi(cr, cgi, txdb = .self$txdb, expr = .self$expr, by = by, ...)
} else {
sid = .self$sample_id[.self$CHIPSEQ[[hm_name]]]
hm_list = lapply(sid, function(x) .self$get_hm(hm_name, x))
names(hm_list) = sid
parent.env(parent.env(e))$enriched_heatmap_list_on_tss_cgi(cr, cgi, txdb = .self$txdb, expr = .self$expr, hm_list = hm_list, hm_name = hm_name, by = by, ...)
}
},
wgbs_qcplot = function(sample_id, chromosome = .self$chromosome) {
methylation_hooks = .self$methylation_hooks
e = environment()
parent.env(parent.env(e))$wgbs_qcplot(sample_id, chromosome)
},
plot_coverage_and_methylation_on_genome = function(sid, chromosome = .self$chromosome, nw = 10000, ...) {
methylation_hooks = .self$methylation_hooks
e = environment()
parent.env(parent.env(e))$plot_coverage_and_methylation_on_genome(sid, chromosome, .self$species, nw, ...)
},
plot_multiple_samples_methylation_on_genome = function(sample_id, chromosome = .self$chromosome, nw = 1000, ...) {
methylation_hooks = .self$methylation_hooks
e = environment()
parent.env(parent.env(e))$plot_multiple_samples_methylation_on_genome(sample_id, annotation = .self$type,
annotation_color = chromosome, species = .self$species, nw = nw, ...)
},
global_methylation_distribution = function(sample_id, chromosome = .self$chromosome, by_chr = FALSE) {
methylation_hooks = .self$methylation_hooks
e = environment()
parent.env(parent.env(e))$global_methylation_distribution(sample_id, annotation = .self$type,
annotation_color = .self$col, chromosome = chromosome, by_chr = by_chr)
},
get_mean_methylation_in_genomic_features = function(sample_id, chromosome = .self$chromosome, gf_list = NULL) {
methylation_hooks = .self$methylation_hooks
e = environment()
parent.env(parent.env(e))$get_mean_methylation_in_genomic_features(sample_id, gf_list = .self$genomic_features[gf_list],
chromosome = chromosome)
},
heatmap_diff_methylation_in_genomic_features = function(gr, ...) {
methylation_hooks = .self$methylation_hooks
e = environment()
parent.env(parent.env(e))$heatmap_diff_methylation_in_genomic_features(gr, annotation = .self$type,
annotation_color = .self$col, txdb = .self$txdb, gf_list = .self$genomic_features, ...)
},
pipeline = function() {
}
)
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