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new feature: implement overlaps
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@Kdreval
Kdreval committed May 13, 2024
1 parent c6b4592 commit 30f327d
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Showing 2 changed files with 150 additions and 55 deletions.
204 changes: 149 additions & 55 deletions R/get_ssm_by_regions.R
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Original file line number Diff line number Diff line change
Expand Up @@ -22,6 +22,9 @@
#' @param projection Obtain variants projected to this reference (one of grch37 or hg38), default is grch37.
#' @param verbose Set to TRUE to maximize the output to console. Default is TRUE.
#' This parameter also dictates the verbosity of any helper function internally called inside the main function.
#' @param engine String indicating which approach to use. Accepted values are
#' "default" (legacy behaviour with for loop for each region) and
#' "overlaps" (more efficient approach using overlaps).
#' @param ... Any additional parameters.
#'
#' @return Returns a data frame of variants in MAF-like format.
Expand Down Expand Up @@ -51,18 +54,18 @@ get_ssm_by_regions = function(these_sample_ids = NULL,
use_name_column = FALSE,
projection = "grch37",
verbose = FALSE,
engine="default",
engine = "default",
...){

# check provided projection
# first, get valid projections
valid_projections = grep("meta", names(GAMBLR.data::sample_data),
valid_projections = grep("meta", names(GAMBLR.data::sample_data),
value = TRUE, invert = TRUE)
if(! projection %in% valid_projections){
stop("Please provide a valid projection. The following are available: ",
paste(valid_projections, collapse=", "), ".")
}

#check if any invalid parameters are provided
check_excess_params(...)

Expand All @@ -79,77 +82,168 @@ get_ssm_by_regions = function(these_sample_ids = NULL,
}else{
regions = regions_list
}

# handle the correct chr prefixing
regions <- gsub("chr", "", regions)
if(projection == "hg38"){
regions <- paste0("chr", regions)
}

if(verbose){
print(regions)
}

#get samples with the dedicated helper function
metadata = id_ease(these_samples_metadata = these_samples_metadata,
these_sample_ids = these_sample_ids,
verbose = verbose,
this_seq_type = this_seq_type)

# The following has these steps to return the maf:
# 1. First check if the maf data is present
# 1a. If maf data is not provided, check whether this_study is specified
# 1b. For both this_study present and absent, check which engine is specified
# 2. If maf data is present, trust that the maf file is pre-defined accordingly
# and no need to handle the this_study parameter explicitly.
# 2a. Check which engine is specified and handle maf_data accordingly

if(missing(maf_data)){
#warn/notify the user what version of this function they are using
message("Using the bundled SSM calls (.maf) calls in GAMBLR.data...")

if(missing(this_study)){
region_mafs = lapply(
regions, function(x){
get_ssm_by_region(
region = x,
these_samples_metadata = metadata,
this_seq_type = this_seq_type,
streamlined = streamlined,
projection = projection,
mode = mode,
verbose = FALSE, #force to FALSE, suppressing noisy output
...
)
if(engine == "overlaps"){
if(verbose){
print("Using the non-default engine for efficiency...")
}
)
}else if(engine == "foverlaps"){
sample_maf = get_ssm_by_samples(these_samples_metadata=these_samples_metadata)
setkey(sample_maf, Chromosome, Start_Position,End_Position)
regions_dt = data.frame(all_lymphome_gene_regions) %>% rownames_to_column("Hugo_Symbol") %>%
separate(all_lymphome_gene_regions,c("Chromosome","region"),sep = ":") %>%
separate(region,c("Start_Position","End_Position"),"-") %>%
mutate(Start_Position=as.numeric(Start_Position),End_Position=as.numeric(End_Position)) %>%
as.data.table()
setkey(regions_dt,Chromosome,Start_Position,End_Position)
maf_regions = foverlaps(sample_maf, regions_dt, type="within", which=TRUE,
by.x=c("Chromosome","Start_Position","End_Position"),
by.y=c("Chromosome","Start_Position","End_Position"))

match_rows=filter(maf_regions,!is.na(yid)) %>% pull(xid)
match_maf = sample_maf[match_rows,]
return(match_maf)

sample_maf <- get_ssm_by_samples(
these_samples_metadata = these_samples_metadata,
this_seq_type = this_seq_type,
projection = projection,
tool_name = mode
)
regions_df <- as.data.frame(regions) %>%
`names<-`("regions") %>%
separate(
regions,
c("Chromosome", "Start_Position","End_Position"),
":|-"
) %>%
mutate(
Start_Position = as.numeric(Start_Position),
End_Position = as.numeric(End_Position)
) %>%
mutate(region = row_number())
region_mafs <- cool_overlaps(
sample_maf,
regions_df
) %>%
dplyr::rename_with(~ gsub(".x", "", .x, fixed = TRUE)) %>%
dplyr::select(all_of(c(names(sample_maf), "region"))) %>%
dplyr::group_split(region)
} else {
region_mafs = lapply(
regions, function(x){
get_ssm_by_region(
region = x,
these_samples_metadata = metadata,
this_seq_type = this_seq_type,
streamlined = streamlined,
projection = projection,
mode = mode,
verbose = FALSE, #force to FALSE, suppressing noisy output
...
)
}
)
}
}else{
region_mafs = lapply(
regions, function(x){
get_ssm_by_region(
region = x,
these_samples_metadata = metadata,
this_seq_type = this_seq_type,
streamlined = streamlined,
projection = projection,
mode = mode,
this_study = this_study,
verbose = FALSE, #force to FALSE, suppressing noisy output
...
)
if(engine == "overlaps"){
if(verbose){
print("Using the non-default engine for efficiency...")
}
)

sample_maf <- get_ssm_by_samples(
these_samples_metadata = these_samples_metadata,
this_seq_type = this_seq_type,
projection = projection,
tool_name = mode,
this_study = this_study
)
regions_df <- as.data.frame(regions) %>%
`names<-`("regions") %>%
separate(
regions,
c("Chromosome", "Start_Position","End_Position"),
":|-"
) %>%
mutate(
Start_Position = as.numeric(Start_Position),
End_Position = as.numeric(End_Position)
) %>%
mutate(region = row_number())

region_mafs <- cool_overlaps(
sample_maf,
regions_df
) %>%
dplyr::rename_with(~ gsub(".x", "", .x, fixed = TRUE)) %>%
dplyr::select(all_of(c(names(sample_maf), "region"))) %>%
dplyr::group_split(region)

} else {
region_mafs = lapply(
regions, function(x){
get_ssm_by_region(
region = x,
these_samples_metadata = metadata,
this_seq_type = this_seq_type,
streamlined = streamlined,
projection = projection,
mode = mode,
this_study = this_study,
verbose = FALSE, #force to FALSE, suppressing noisy output
...
)
}
)
}
}
}else{
region_mafs = lapply(regions, function(x){get_ssm_by_region(region = x,
maf_data = maf_data,
these_samples_metadata = metadata,
this_seq_type = this_seq_type,
streamlined = streamlined,
projection = projection,
verbose = FALSE)})
if(engine == "overlaps"){
if(verbose){
print("Using the non-default engine for efficiency...")
}
regions_df <- as.data.frame(regions) %>%
`names<-`("regions") %>%
separate(
regions,
c("Chromosome", "Start_Position","End_Position"),
":|-"
) %>%
mutate(
Start_Position = as.numeric(Start_Position),
End_Position = as.numeric(End_Position)
) %>%
mutate(region = row_number())

region_mafs <- cool_overlaps(
sample_maf,
regions_df
) %>%
dplyr::rename_with(~ gsub(".x", "", .x, fixed = TRUE)) %>%
dplyr::select(all_of(c(names(sample_maf), "region"))) %>%
dplyr::group_split(region)
}else{
region_mafs = lapply(regions, function(x){get_ssm_by_region(region = x,
maf_data = maf_data,
these_samples_metadata = metadata,
this_seq_type = this_seq_type,
streamlined = streamlined,
projection = projection,
verbose = FALSE)})
}
}

#deal with region names
Expand Down
1 change: 1 addition & 0 deletions man/get_ssm_by_regions.Rd
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