R/MMRFclinical.R
In marziasettino/MMRFBiolinks: R package for integrative analysis of MMRF-CoMMpass data
Defines functions
MMRFRG_GetBorInfo
MMRFRG_GetIDByBor
MMRFRG_GetBorByID
MMRFGDC_QuerySamples
get_IDall
MMRFGDC_GetIdentifierByTherapy
MMRFGDC_QuerySampleTypes
MMRFGDC_GetTherapyByID
MMRFGDC_GetTreatments
MMRFGDC_QueryClinic
#' @title MMRFGDC_QueryClinic
#' @description
#' MMRFGDC_QueryClinic downloads and prepares all clinical information from API
#'
#' @param type A valid type. Options "clinical", "Biospecimen" (see list with getGDCprojects()$project_id)]
#' @param save.csv Write clinical information into a csv document
#' @export
#' @importFrom data.table rbindlist as.data.table
#' @importFrom jsonlite fromJSON
#' @importFrom TCGAbiolinks GDCquery_clinic
#' @examples
#' clin.mm<-MMRFGDC_QueryClinic(type = "clinical")
#' clin.mm<-MMRFGDC_QueryClinic(type = "Biospecimen")
#' @return A data frame with the clinical information
MMRFGDC_QueryClinic<- function(type = "clinical", save.csv = FALSE){
clin<-GDCquery_clinic(project="MMRF-COMMPASS", type, save.csv)
#names(clin)[names(clin) == 'submitter_id'] <- 'bcr_patient_barcode'
#if clinical
if (type!="clinical" & type!="Biospecimen" ){
return("Error message: type does not exist")
}
if (type=="clinical"){
names(clin)[1] <- "bcr_patient_barcode"
}
else if (type=="Biospecimen"){
bcr_patient_barcode.sub<-clin[colnames(clin)=='submitter_id']
colnames(bcr_patient_barcode.sub)[1]<-"bcr_patient_barcode"
bcr_patient_barcode.sub$bcr_patient_barcode<-substr(bcr_patient_barcode.sub$bcr_patient_barcode,1,9)
clin<-cbind(bcr_patient_barcode.sub,clin)
}
return(clin)
}
#' @title Get list of treatments
#' @description
#' get treatment list from clinical data
#' @param clin.mm is a data.frame containing clinical information from GDC Data Portal
#' (e.g.data days_to_death ,' days_to_last_follow_up , vital_status, etc)
#' @examples
#' treat.list<-MMRFGDC_GetTreatments(clin.mm)
#' @export
#' @return a data.frame
MMRFGDC_GetTreatments<- function(clin.mm){
df<-NULL
treat.list<-clin.mm$treatments
for(i in 1:length(treat.list)){
treat.aux<-as.data.frame(treat.list[[i]])
barcode<-substring(treat.aux$submitter_id,1,9)
treat<-treat.aux$therapeutic_agents
line<-treat.aux$regimen_or_line_of_therapy
df<-rbind(df, data.frame(barcode,treat,line))
}
return(unique(df))
}
#' @title MMRFGDC_GetTherapyByID
#' @description
#' Get information about Therapy filtered by sample identifier
#' @param clin.mm is a data.frame containing clinical information from GDC Data Portal
#' (e.g.data days_to_death ,' days_to_last_follow_up , vital_status, etc)
#' @examples
#' listSamples <- c("MMRF_1951","MMRF_1474",
#' "MMRF_2709","MMRF_2199",
#' "MMRF_1216","MMRF_2119",
#' "MMRF_2546","MMRF_2613",
#' "MMRF_1647","MMRF_2170")
#' therapy.info<-MMRFGDC_GetTherapyByID(listSamples, clin.mm)
#' @export
#' @return a data.frame
MMRFGDC_GetTherapyByID<- function(listSamples,clin.mm){
clin.mm<-clin.mm[,c("bcr_patient_barcode","treatments")]
clin.mm.filt<-NULL
clin.mm.trt<-NULL
for(i in 1:length(listSamples)){
clin.mm.filt.aux<-clin.mm[clin.mm$bcr_patient_barcode==listSamples[i],]
clin.mm.filt<-rbind(clin.mm.filt, clin.mm.filt.aux)
}
for(i in 1:length(clin.mm.filt)){
# clin.mm.bar<-clin.mm.aux$bcr_patient_barcode
clin.mm.trt.aux<-clin.mm.filt$treatments[[i]]
clin.mm.trt<-rbind(clin.mm.trt,clin.mm.trt.aux)
}
clin.mm.trt<-clin.mm.trt[,c("submitter_id","therapeutic_agents","regimen_or_line_of_therapy","days_to_treatment_start","days_to_treatment_end")]
return(clin.mm.trt)
}
#----------------------------------------
#' @title MMRFGDC_QuerySampleTypes
#' @description
#' Retrieve samples identifiers from GDCquery output for filtering them by the selected type sample
#' @param query the resuting dataframe of GDCquery
#' @param typesample a character vector indicating tissue type to query.
#' Example:
#' \tabular{ll}{
#'TBM \tab Primary Blood Derived Cancer-Bone Marrow \cr
#'TRBM \tab Recurrent Blood Derived Cancer-Bone Marrow \cr
#'TB \tab Primary Blood Derived Cancer-Peripheral Blood \cr
#'TRB \tab Recurrent Blood Derived Cancer - Peripheral Blood \cr
#'}
#' @examples
#' \dontrun{
#' query <- GDCquery(project = "MMRF-COMMPASS",
#' data.category = "Transcriptome Profiling",
#' data.type = "Gene Expression Quantification",
#' experimental.strategy = "RNA-Seq",
#' workflow.type="HTSeq - FPKM")
#'
#'
#'tsample<-"TRBM"
#'MMRFGDC_QuerySampleTypes(query,tsample)
#'MMRFGDC_QuerySampleTypes(query,c("TB","TRBM"))
#'
#'
#' }
#'@return a list of samples identifiers filtered by type sample selected
MMRFGDC_QuerySampleTypes <- function(query,typesample){
if(is.null(query) || is.null(typesample)){
stop("Please provide arguments as explained in the integrated vignette.")
}
typesample.cn<- c("Primary Blood Derived Cancer - Bone Marrow",
"Recurrent Blood Derived Cancer - Bone Marrow",
"Primary Blood Derived Cancer - Peripheral Blood",
"Recurrent Blood Derived Cancer - Peripheral Blood")
typesample.sn <- c("TBM","TRBM","TB","TRB")
df.typesample <- data.frame(typesample.sn, typesample.cn)
results<- getResults(query,cols=c("sample_type","cases"))
identifier.all<-NULL
for (typesample.i in 1:length(typesample)) {
if(typesample[typesample.i] %in% df.typesample$typesample.sn ){
temp<-df.typesample[df.typesample$typesample.sn==typesample[typesample.i],]
filt<-results[results$sample_type==temp$typesample.cn,]
identifier.all<-unique(substring(filt$cases,1,9))
} else {
return("Error message: one or more sample types do not exist")
}
}
return(identifier.all)
}
#' @title MMRFGDC_GetIdentifierByTherapy
#' @description
#' Search patient clinical information filtered by therapy name
#' @param therapyname Therapy name
#' @param clin.mm is a data.frame using function 'clinic' with information
#' related to identifier / samples such as bcr_patient_barcode, days_to_death ,
#' days_to_last_follow_up , vital_status, etc
#' @import dplyr
#' @export
#' @examples
#' clin.mm<-MMRFGDC_QueryClinic(type = "clinical")
#' identifier.dexa<-MMRFGDC_GetIdentifierByTherapy("Dexamethasone",clin.mm)
#' @return a character vector with samples identifiers
MMRFGDC_GetIdentifierByTherapy<- function(therapyname,clin.mm){
if(is.null(therapyname) || is.null(clin.mm)){
stop("Please provide arguments as explained in the integrated vignette.")
}
treat.tab<-MMRFGetGDC_Treatments(clin.mm)
for (i in 1:length(therapyname)) {
df<-na.omit(treat.tab[treat.tab$treat==therapyname[i],])
}
return(unique(df$barcode))
}
#...................................new...............................
get_IDall<- function(query,typesample, clin.mm,therapyname){
id1<-MMRFGDC_GetIdentifierByTherapy(therapyname,clin.mm)
id2<-MMRFGDC_QuerySampleTypes(query,typesample)
id<-intersect(id1,id2)
return(id)
}
#' @title MMRFGDC_QuerySamples
#' @description
#' Retrieve samples identifiers filtered by the selected type sample (case 2) or
#' Retrieve samples identifiers filtered by the selected therapy (case 3) or
#' Retrieve samples identifiers from both case 1 and case 2
#' @param query the resuting dataframe of GDCquery
#' @param typesample a character vector indicating tissue type to query.
#' Example:
#' \tabular{ll}{
#'TBM \tab Primary Blood Derived Cancer-Bone Marrow \cr
#'TRBM \tab Recurrent Blood Derived Cancer-Bone Marrow \cr
#'TB \tab Primary Blood Derived Cancer-Peripheral Blood \cr
#'TRB \tab Recurrent Blood Derived Cancer - Peripheral Blood \cr
#'}
#' @export
#' @examples
#' \dontrun{
#' therapy<-"Dexamethasone"
#'
#' tsample<-"TRBM"
#' clin<-MMRFGDC_QueryClinic(type = "clinical")
#'
#' query.mm <- GDCquery(project = "MMRF-COMMPASS",
#' data.category = "Transcriptome Profiling",
#' data.type = "Gene Expression Quantification",
#' experimental.strategy = "RNA-Seq",
#' workflow.type="HTSeq - FPKM")
#'
#'
#'
#' IDs<-MMRFGDC_QuerySamples(query=query.mm,typesample=tsample, clin.mm=clin,therapyname=therapy) #case 1
#' IDs<-MMRFGDC_QuerySamples(query=query.mm,typesample=tsample) #case 2
#' IDs<-MMRFGDC_QuerySamples(clin.mm=clin,therapyname=therapy) #case 3
#'
#' }
#'@return a list of samples identifiers
MMRFGDC_QuerySamples <- function(...){
args<-list(...)
mc <- match.call(expand.dots = TRUE )
print(names(mc))
if(length(args)== 0 || (length(args) %% 2)!=0 ){
stop("Please provide arguments as explained in the integrated vignette.")
}
id.all<-NULL
if(length(args)== 4){
id.all<-get_IDall(...)
print("Return sample ID filtered by sample type and therapy.")
return(id.all)
}
if("query" %in% names(mc) & "typesample" %in% names(mc) ){
id.all<-MMRFGDC_QuerySampleTypes(...)
print("Return sample ID filtered by sample type.")
}
else{
if("clin.mm" %in% names(mc) & "therapyname" %in% names(mc)){
id.all<-MMRFGDC_GetIdentifierByTherapy(...)
print("Return sample ID filtered by therapy.")
}
}
return(id.all)
}
#' @title MMRFRG_GetBorByID
#' @description
#' Get Best Overall response filtered by sample identifier
#' @param identifier is a vector of samples identifiers
#' @param trt.resp is a data.frame of clinical information downloaded from MMRF-Commpass Researcher Gateway
#' and imported into R environment
#' @examples
#' list.samp<- c("MMRF_0001","MMRF_0002",
#' "MMRF_0003","MMRF_0004",
#' "MMRF_0005","MMRF_0006",
#' "MMRF_0007","MMRF_0008",
#' "MMRF_0009","MMRF_0010")
#'
#' bestOverall<-MMRFRG_GetBorByID(clinMMGateway,list.samp)
#' @return a dataframe
MMRFRG_GetBorByID<- function(treat.resp,identifier){
inter<-intersect(identifier,treat.resp$public_id)
filt<-treat.resp[treat.resp$public_id %in% inter,]
filt<-filt[,c("public_id","trtname","trtshnm","bestresp","bestrespsh")]
return(unique(filt))
}
#' @title MMRFRG_GetIDByBor
#' @description
#' Get clinical data filtered by Best Overall Response (BOR) type
#' @param bor is the type of Best Overall Response (BOR)
#' Example:
#' \tabular{ll}{
#'CR \tab Complete Response \cr
#'PR \tab Partial Response \cr
#'VGPR \tab Very Good Partial Response \cr
#'SD \tab Stable Disease \cr
#'PD \tab Progressive Disease \cr
#'sCR \tab Stringent Complete Response \cr
#'}
#' @param trt.resp is a data.frame of clinical information downloaded from MMRF-Commpass Researcher Gateway
#' and imported into R environment
#' @examples
#' bestOverallType<-MMRFRG_GetIDByBor(clinMMGateway,"PR")
#' @return a dataframe
MMRFRG_GetIDByBor<- function(treat.resp, bor){
code <- c("CR","PR","VGPR","SD","PD","sCR")
bestresp<-c("Complete Response","Partial Response", "Very Good Partial Response",
"Stable Disease", "Progressive Disease", "Stringent Complete Response")
table.bor <- data.frame(code, bestresp)
if(!bor %in% table.bor$code)
stop("Please set a valid argument for bor parameter: CR, PR, VGPR, SD, PD, sCR")
filt<-treat.resp[treat.resp$bestrespsh==bor,]
return(filt)
}
#' @title MMRFRG_GetBorInfo
#' @description
#' Get Best Overall Response (BOR) type filtered by sample ID (Case 1) or
#' Get sample ID filtered by BOR type (Case 2)
#' @param bor is the type of Best Overall Response (BOR)
#' Example:
#' \tabular{ll}{
#'CR \tab Complete Response \cr
#'PR \tab Partial Response \cr
#'VGPR \tab Very Good Partial Response \cr
#'SD \tab Stable Disease \cr
#'PD \tab Progressive Disease \cr
#'sCR \tab Stringent Complete Response \cr
#'}
#' @param trt.resp is a data.frame of clinical information downloaded from MMRF-Commpass Researcher Gateway
#' and imported into R environment
#' @param listSamples is a vector of samples identifiers
#' @export
#' @examples
#' # case 1
#'
#' IDsamples<-MMRFRG_GetBorInfo(clin.rg=clinMMGateway,bor="PR")
#'
#' # case 2
#'
#' list.samp<- c("MMRF_0001","MMRF_0002",
#' "MMRF_0003","MMRF_0004",
#' "MMRF_0005","MMRF_0006",
#' "MMRF_0007","MMRF_0008",
#' "MMRF_0009","MMRF_0010")
#'
#'
#' bestOverall<-MMRFRG_GetBorInfo(clin.rg=clinMMGateway,listSamples=list.samp)
#' @export
#' @return a dataframe
MMRFRG_GetBorInfo<- function(clin.rg,...){
args<-list(...)
mc <- match.call(expand.dots = TRUE )
print(names(mc))
res<-NULL
if(length(args)!= 1){
stop("Please provide arguments as explained in the integrated vignette.")
}
if("listSamples" %in% names(mc)){
res<-MMRFRG_GetBorByID(clin.rg,args[[1]])
print("Return BOR filtered by sample ID.")
}
else{
if("bor" %in% names(mc) ){
res<- MMRFRG_GetIDByBor(clin.rg,args[[1]])
print("Return sample ID filtered by BOR type.")
}
}
return(res)
}
marziasettino/MMRFBiolinks documentation built on Jan. 24, 2023, 4:49 a.m.
R Package Documentation
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Defines functions MMRFRG_GetBorInfo MMRFRG_GetIDByBor MMRFRG_GetBorByID MMRFGDC_QuerySamples get_IDall MMRFGDC_GetIdentifierByTherapy MMRFGDC_QuerySampleTypes MMRFGDC_GetTherapyByID MMRFGDC_GetTreatments MMRFGDC_QueryClinic
#' @title MMRFGDC_QueryClinic
#' @description
#' MMRFGDC_QueryClinic downloads and prepares all clinical information from API
#'
#' @param type A valid type. Options "clinical", "Biospecimen" (see list with getGDCprojects()$project_id)]
#' @param save.csv Write clinical information into a csv document
#' @export
#' @importFrom data.table rbindlist as.data.table
#' @importFrom jsonlite fromJSON
#' @importFrom TCGAbiolinks GDCquery_clinic
#' @examples
#' clin.mm<-MMRFGDC_QueryClinic(type = "clinical")
#' clin.mm<-MMRFGDC_QueryClinic(type = "Biospecimen")
#' @return A data frame with the clinical information
MMRFGDC_QueryClinic<- function(type = "clinical", save.csv = FALSE){
clin<-GDCquery_clinic(project="MMRF-COMMPASS", type, save.csv)
#names(clin)[names(clin) == 'submitter_id'] <- 'bcr_patient_barcode'
#if clinical
if (type!="clinical" & type!="Biospecimen" ){
return("Error message: type does not exist")
}
if (type=="clinical"){
names(clin)[1] <- "bcr_patient_barcode"
}
else if (type=="Biospecimen"){
bcr_patient_barcode.sub<-clin[colnames(clin)=='submitter_id']
colnames(bcr_patient_barcode.sub)[1]<-"bcr_patient_barcode"
bcr_patient_barcode.sub$bcr_patient_barcode<-substr(bcr_patient_barcode.sub$bcr_patient_barcode,1,9)
clin<-cbind(bcr_patient_barcode.sub,clin)
}
return(clin)
}
#' @title Get list of treatments
#' @description
#' get treatment list from clinical data
#' @param clin.mm is a data.frame containing clinical information from GDC Data Portal
#' (e.g.data days_to_death ,' days_to_last_follow_up , vital_status, etc)
#' @examples
#' treat.list<-MMRFGDC_GetTreatments(clin.mm)
#' @export
#' @return a data.frame
MMRFGDC_GetTreatments<- function(clin.mm){
df<-NULL
treat.list<-clin.mm$treatments
for(i in 1:length(treat.list)){
treat.aux<-as.data.frame(treat.list[[i]])
barcode<-substring(treat.aux$submitter_id,1,9)
treat<-treat.aux$therapeutic_agents
line<-treat.aux$regimen_or_line_of_therapy
df<-rbind(df, data.frame(barcode,treat,line))
}
return(unique(df))
}
#' @title MMRFGDC_GetTherapyByID
#' @description
#' Get information about Therapy filtered by sample identifier
#' @param clin.mm is a data.frame containing clinical information from GDC Data Portal
#' (e.g.data days_to_death ,' days_to_last_follow_up , vital_status, etc)
#' @examples
#' listSamples <- c("MMRF_1951","MMRF_1474",
#' "MMRF_2709","MMRF_2199",
#' "MMRF_1216","MMRF_2119",
#' "MMRF_2546","MMRF_2613",
#' "MMRF_1647","MMRF_2170")
#' therapy.info<-MMRFGDC_GetTherapyByID(listSamples, clin.mm)
#' @export
#' @return a data.frame
MMRFGDC_GetTherapyByID<- function(listSamples,clin.mm){
clin.mm<-clin.mm[,c("bcr_patient_barcode","treatments")]
clin.mm.filt<-NULL
clin.mm.trt<-NULL
for(i in 1:length(listSamples)){
clin.mm.filt.aux<-clin.mm[clin.mm$bcr_patient_barcode==listSamples[i],]
clin.mm.filt<-rbind(clin.mm.filt, clin.mm.filt.aux)
}
for(i in 1:length(clin.mm.filt)){
# clin.mm.bar<-clin.mm.aux$bcr_patient_barcode
clin.mm.trt.aux<-clin.mm.filt$treatments[[i]]
clin.mm.trt<-rbind(clin.mm.trt,clin.mm.trt.aux)
}
clin.mm.trt<-clin.mm.trt[,c("submitter_id","therapeutic_agents","regimen_or_line_of_therapy","days_to_treatment_start","days_to_treatment_end")]
return(clin.mm.trt)
}
#----------------------------------------
#' @title MMRFGDC_QuerySampleTypes
#' @description
#' Retrieve samples identifiers from GDCquery output for filtering them by the selected type sample
#' @param query the resuting dataframe of GDCquery
#' @param typesample a character vector indicating tissue type to query.
#' Example:
#' \tabular{ll}{
#'TBM \tab Primary Blood Derived Cancer-Bone Marrow \cr
#'TRBM \tab Recurrent Blood Derived Cancer-Bone Marrow \cr
#'TB \tab Primary Blood Derived Cancer-Peripheral Blood \cr
#'TRB \tab Recurrent Blood Derived Cancer - Peripheral Blood \cr
#'}
#' @examples
#' \dontrun{
#' query <- GDCquery(project = "MMRF-COMMPASS",
#' data.category = "Transcriptome Profiling",
#' data.type = "Gene Expression Quantification",
#' experimental.strategy = "RNA-Seq",
#' workflow.type="HTSeq - FPKM")
#'
#'
#'tsample<-"TRBM"
#'MMRFGDC_QuerySampleTypes(query,tsample)
#'MMRFGDC_QuerySampleTypes(query,c("TB","TRBM"))
#'
#'
#' }
#'@return a list of samples identifiers filtered by type sample selected
MMRFGDC_QuerySampleTypes <- function(query,typesample){
if(is.null(query) || is.null(typesample)){
stop("Please provide arguments as explained in the integrated vignette.")
}
typesample.cn<- c("Primary Blood Derived Cancer - Bone Marrow",
"Recurrent Blood Derived Cancer - Bone Marrow",
"Primary Blood Derived Cancer - Peripheral Blood",
"Recurrent Blood Derived Cancer - Peripheral Blood")
typesample.sn <- c("TBM","TRBM","TB","TRB")
df.typesample <- data.frame(typesample.sn, typesample.cn)
results<- getResults(query,cols=c("sample_type","cases"))
identifier.all<-NULL
for (typesample.i in 1:length(typesample)) {
if(typesample[typesample.i] %in% df.typesample$typesample.sn ){
temp<-df.typesample[df.typesample$typesample.sn==typesample[typesample.i],]
filt<-results[results$sample_type==temp$typesample.cn,]
identifier.all<-unique(substring(filt$cases,1,9))
} else {
return("Error message: one or more sample types do not exist")
}
}
return(identifier.all)
}
#' @title MMRFGDC_GetIdentifierByTherapy
#' @description
#' Search patient clinical information filtered by therapy name
#' @param therapyname Therapy name
#' @param clin.mm is a data.frame using function 'clinic' with information
#' related to identifier / samples such as bcr_patient_barcode, days_to_death ,
#' days_to_last_follow_up , vital_status, etc
#' @import dplyr
#' @export
#' @examples
#' clin.mm<-MMRFGDC_QueryClinic(type = "clinical")
#' identifier.dexa<-MMRFGDC_GetIdentifierByTherapy("Dexamethasone",clin.mm)
#' @return a character vector with samples identifiers
MMRFGDC_GetIdentifierByTherapy<- function(therapyname,clin.mm){
if(is.null(therapyname) || is.null(clin.mm)){
stop("Please provide arguments as explained in the integrated vignette.")
}
treat.tab<-MMRFGetGDC_Treatments(clin.mm)
for (i in 1:length(therapyname)) {
df<-na.omit(treat.tab[treat.tab$treat==therapyname[i],])
}
return(unique(df$barcode))
}
#...................................new...............................
get_IDall<- function(query,typesample, clin.mm,therapyname){
id1<-MMRFGDC_GetIdentifierByTherapy(therapyname,clin.mm)
id2<-MMRFGDC_QuerySampleTypes(query,typesample)
id<-intersect(id1,id2)
return(id)
}
#' @title MMRFGDC_QuerySamples
#' @description
#' Retrieve samples identifiers filtered by the selected type sample (case 2) or
#' Retrieve samples identifiers filtered by the selected therapy (case 3) or
#' Retrieve samples identifiers from both case 1 and case 2
#' @param query the resuting dataframe of GDCquery
#' @param typesample a character vector indicating tissue type to query.
#' Example:
#' \tabular{ll}{
#'TBM \tab Primary Blood Derived Cancer-Bone Marrow \cr
#'TRBM \tab Recurrent Blood Derived Cancer-Bone Marrow \cr
#'TB \tab Primary Blood Derived Cancer-Peripheral Blood \cr
#'TRB \tab Recurrent Blood Derived Cancer - Peripheral Blood \cr
#'}
#' @export
#' @examples
#' \dontrun{
#' therapy<-"Dexamethasone"
#'
#' tsample<-"TRBM"
#' clin<-MMRFGDC_QueryClinic(type = "clinical")
#'
#' query.mm <- GDCquery(project = "MMRF-COMMPASS",
#' data.category = "Transcriptome Profiling",
#' data.type = "Gene Expression Quantification",
#' experimental.strategy = "RNA-Seq",
#' workflow.type="HTSeq - FPKM")
#'
#'
#'
#' IDs<-MMRFGDC_QuerySamples(query=query.mm,typesample=tsample, clin.mm=clin,therapyname=therapy) #case 1
#' IDs<-MMRFGDC_QuerySamples(query=query.mm,typesample=tsample) #case 2
#' IDs<-MMRFGDC_QuerySamples(clin.mm=clin,therapyname=therapy) #case 3
#'
#' }
#'@return a list of samples identifiers
MMRFGDC_QuerySamples <- function(...){
args<-list(...)
mc <- match.call(expand.dots = TRUE )
print(names(mc))
if(length(args)== 0 || (length(args) %% 2)!=0 ){
stop("Please provide arguments as explained in the integrated vignette.")
}
id.all<-NULL
if(length(args)== 4){
id.all<-get_IDall(...)
print("Return sample ID filtered by sample type and therapy.")
return(id.all)
}
if("query" %in% names(mc) & "typesample" %in% names(mc) ){
id.all<-MMRFGDC_QuerySampleTypes(...)
print("Return sample ID filtered by sample type.")
}
else{
if("clin.mm" %in% names(mc) & "therapyname" %in% names(mc)){
id.all<-MMRFGDC_GetIdentifierByTherapy(...)
print("Return sample ID filtered by therapy.")
}
}
return(id.all)
}
#' @title MMRFRG_GetBorByID
#' @description
#' Get Best Overall response filtered by sample identifier
#' @param identifier is a vector of samples identifiers
#' @param trt.resp is a data.frame of clinical information downloaded from MMRF-Commpass Researcher Gateway
#' and imported into R environment
#' @examples
#' list.samp<- c("MMRF_0001","MMRF_0002",
#' "MMRF_0003","MMRF_0004",
#' "MMRF_0005","MMRF_0006",
#' "MMRF_0007","MMRF_0008",
#' "MMRF_0009","MMRF_0010")
#'
#' bestOverall<-MMRFRG_GetBorByID(clinMMGateway,list.samp)
#' @return a dataframe
MMRFRG_GetBorByID<- function(treat.resp,identifier){
inter<-intersect(identifier,treat.resp$public_id)
filt<-treat.resp[treat.resp$public_id %in% inter,]
filt<-filt[,c("public_id","trtname","trtshnm","bestresp","bestrespsh")]
return(unique(filt))
}
#' @title MMRFRG_GetIDByBor
#' @description
#' Get clinical data filtered by Best Overall Response (BOR) type
#' @param bor is the type of Best Overall Response (BOR)
#' Example:
#' \tabular{ll}{
#'CR \tab Complete Response \cr
#'PR \tab Partial Response \cr
#'VGPR \tab Very Good Partial Response \cr
#'SD \tab Stable Disease \cr
#'PD \tab Progressive Disease \cr
#'sCR \tab Stringent Complete Response \cr
#'}
#' @param trt.resp is a data.frame of clinical information downloaded from MMRF-Commpass Researcher Gateway
#' and imported into R environment
#' @examples
#' bestOverallType<-MMRFRG_GetIDByBor(clinMMGateway,"PR")
#' @return a dataframe
MMRFRG_GetIDByBor<- function(treat.resp, bor){
code <- c("CR","PR","VGPR","SD","PD","sCR")
bestresp<-c("Complete Response","Partial Response", "Very Good Partial Response",
"Stable Disease", "Progressive Disease", "Stringent Complete Response")
table.bor <- data.frame(code, bestresp)
if(!bor %in% table.bor$code)
stop("Please set a valid argument for bor parameter: CR, PR, VGPR, SD, PD, sCR")
filt<-treat.resp[treat.resp$bestrespsh==bor,]
return(filt)
}
#' @title MMRFRG_GetBorInfo
#' @description
#' Get Best Overall Response (BOR) type filtered by sample ID (Case 1) or
#' Get sample ID filtered by BOR type (Case 2)
#' @param bor is the type of Best Overall Response (BOR)
#' Example:
#' \tabular{ll}{
#'CR \tab Complete Response \cr
#'PR \tab Partial Response \cr
#'VGPR \tab Very Good Partial Response \cr
#'SD \tab Stable Disease \cr
#'PD \tab Progressive Disease \cr
#'sCR \tab Stringent Complete Response \cr
#'}
#' @param trt.resp is a data.frame of clinical information downloaded from MMRF-Commpass Researcher Gateway
#' and imported into R environment
#' @param listSamples is a vector of samples identifiers
#' @export
#' @examples
#' # case 1
#'
#' IDsamples<-MMRFRG_GetBorInfo(clin.rg=clinMMGateway,bor="PR")
#'
#' # case 2
#'
#' list.samp<- c("MMRF_0001","MMRF_0002",
#' "MMRF_0003","MMRF_0004",
#' "MMRF_0005","MMRF_0006",
#' "MMRF_0007","MMRF_0008",
#' "MMRF_0009","MMRF_0010")
#'
#'
#' bestOverall<-MMRFRG_GetBorInfo(clin.rg=clinMMGateway,listSamples=list.samp)
#' @export
#' @return a dataframe
MMRFRG_GetBorInfo<- function(clin.rg,...){
args<-list(...)
mc <- match.call(expand.dots = TRUE )
print(names(mc))
res<-NULL
if(length(args)!= 1){
stop("Please provide arguments as explained in the integrated vignette.")
}
if("listSamples" %in% names(mc)){
res<-MMRFRG_GetBorByID(clin.rg,args[[1]])
print("Return BOR filtered by sample ID.")
}
else{
if("bor" %in% names(mc) ){
res<- MMRFRG_GetIDByBor(clin.rg,args[[1]])
print("Return sample ID filtered by BOR type.")
}
}
return(res)
}
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