inst/unitTests/test_select.R
In ju-mu/PANTHER.db: A set of annotation maps describing the entire PANTHER Gene Ontology
#### Prepare reference queries from PANTHER webservice 18.09.2013 ####
#results will be used for Unit Tests
require(PANTHER.db)
if(F){
library(RCurl)
require(RUnit)
url <- 'http://www.pantherdb.org/webservices/garuda/search.jsp?keyword='
ids <- PANTHER.db::keys(PANTHER.db,"UNIPROT")[c(50,111,444)];ids
fullUrl <- paste0(url,paste(ids[[3]], collapse="|"),'&listType=gene&type=getList')#only one allowed
gs <- read.delim(fullUrl,stringsAsFactors=F)$Gene.Symbol
fullUrl <- paste0(url,paste(ids, collapse="+or+"),'&listType=pathway&type=getList')
path_acc <- read.delim(fullUrl,stringsAsFactors=F)$Pathway.Accession
fullUrl <- paste0(url,paste(ids, collapse="+or+"),'&listType=family&type=getList')
fam_acc <- read.delim(fullUrl,stringsAsFactors=F)$Family.Accession
fullUrl <- paste0(url,paste(ids, collapse="+or+"),'&listType=category&type=getList')
cat_acc <- read.delim(fullUrl,stringsAsFactors=F)$Category.Accession
}
### ###
test_structure <- function(){
RUnit::checkEquals(sort(PANTHER.db::keytypes(PANTHER.db)),sort(PANTHER.db:::.keytypes()))
RUnit::checkEquals(sort(PANTHER.db::keys(PANTHER.db)),sort(PANTHER.db:::.keys(PANTHER.db,"FAMILY_ID")))
RUnit::checkEquals(sort(PANTHER.db::columns(PANTHER.db)),sort(PANTHER.db:::.cols()))
}
online <- FALSE
test_select_vs_webquery <- function(){
ids <- "PTHR10763:SF23"#webserver returns go cats and class ids for all subfamilies
webquery <- sprintf("http://www.pantherdb.org/webservices/garuda/search.jsp?keyword=%s&listType=category&type=getList",ids)
if(online){
res <- read.delim(webquery) #webquery result on 02.02.2021 with v16.0:
dput(sort(as.character(res$Category.Accession)))
}
response.acc <- c("GO:0000075", "GO:0000076", "GO:0000086", "GO:0000228", "GO:0000278",
"GO:0000280", "GO:0000781", "GO:0000784", "GO:0000808", "GO:0003676",
"GO:0003677", "GO:0003688", "GO:0003690", "GO:0005488", "GO:0005622",
"GO:0005634", "GO:0005664", "GO:0005694", "GO:0006139", "GO:0006259",
"GO:0006260", "GO:0006261", "GO:0006270", "GO:0006725", "GO:0006807",
"GO:0006996", "GO:0007049", "GO:0007093", "GO:0007346", "GO:0008152",
"GO:0009058", "GO:0009059", "GO:0009987", "GO:0010389", "GO:0010564",
"GO:0010948", "GO:0010972", "GO:0016043", "GO:0018130", "GO:0019438",
"GO:0022402", "GO:0031570", "GO:0031974", "GO:0031981", "GO:0032991",
"GO:0033314", "GO:0034641", "GO:0034645", "GO:0034654", "GO:0043170",
"GO:0043226", "GO:0043227", "GO:0043228", "GO:0043229", "GO:0043231",
"GO:0043232", "GO:0043233", "GO:0043565", "GO:0044237", "GO:0044238",
"GO:0044249", "GO:0044260", "GO:0044271", "GO:0044770", "GO:0044772",
"GO:0044774", "GO:0044818", "GO:0044839", "GO:0045786", "GO:0045930",
"GO:0046483", "GO:0048285", "GO:0048519", "GO:0048523", "GO:0050789",
"GO:0050794", "GO:0051726", "GO:0065007", "GO:0070013", "GO:0071704",
"GO:0071840", "GO:0071897", "GO:0090304", "GO:0097159", "GO:0098687",
"GO:0110165", "GO:0140014", "GO:1901360", "GO:1901362", "GO:1901363",
"GO:1901576", "GO:1901987", "GO:1901988", "GO:1901990", "GO:1901991",
"GO:1902749", "GO:1902750", "GO:1903047", "GO:1990837", "PC00199")
select_res <- sort( c( PANTHER.db::select(PANTHER.db,keys=ids,columns="GOSLIM_ID")$GOSLIM_ID, PANTHER.db::select(PANTHER.db,keys=ids,columns="CLASS_ID")$CLASS_ID ) )
RUnit::checkEquals(response.acc,select_res)
ids <- "PC00015"
if(online){
webquery <- sprintf("http://www.pantherdb.org/webservices/garuda/search.jsp?keyword=%s&listType=family&type=getList",ids)
res <- read.delim(webquery) # webquery result on 02.02.2021 with v16.0:
dput(sort(as.character(res$Family.Accession)))
}
webquery_res <- c("PTHR11352", "PTHR11352:SF0", "PTHR11352:SF10", "PTHR11352:SF11",
"PTHR11352:SF12", "PTHR11352:SF3", "PTHR11352:SF5", "PTHR11352:SF6",
"PTHR11352:SF8", "PTHR11352:SF9")
select_res <- sort(PANTHER.db::select(PANTHER.db,keys=ids,columns="FAMILY_ID",keytype="CLASS_ID")$FAMILY_ID)
RUnit::checkEquals(webquery_res,select_res)
ids <- "Q90Z00" # PTHR24416:SF131
# DANRE|ZFIN=ZDB-GENE-980526-255|UniProtKB=Q90Z00 Q90Z00 fgfr1a PTHR24416:SF131 TYROSINE-PROTEIN KINASE RECEPTOR
# FGF signaling pathway#P00021>FGFR1-4#P00636;Angiogenesis#P00005>FGFR-1#P00186
if(online){
webquery <- sprintf("http://www.pantherdb.org/webservices/garuda/search.jsp?keyword=%s&listType=pathway&type=getList",paste(ids,collapse="+or+"))
res <- read.delim(webquery) # webquery result on 02.02.2021 with v16.0:
dput(sort(as.character(res$Pathway.Accession)))
}
webquery_res <- c("P00005", "P00021")
# this also returns NA, as there is no Pathway association to Family terms, just to subfamilies!
# BUT:
# From PANTHER authors on 15.10.2019:
# The sequence association file provides direct association of data to the pathway, while keyword search uses rather loose criteria to return results. In your example, the family is an indirect (or inferred) association to the pathway, and thus not included in the sequence association file. The inferred data are allowed in web search or browsing, but not included in any statistical tools. Therefore, they are not included in the sequence association files either.
#
# Hope this helps.
#
# Thanks,
#
# PANTHER feedback
select_res <- sort(PANTHER.db::select(PANTHER.db,keys=ids,columns="PATHWAY_ID",keytype = "UNIPROT")$PATHWAY_ID)
select_res2 <- sort(AnnotationDbi::mapIds(PANTHER.db,keys=ids,column="PATHWAY_ID",keytype="UNIPROT",multiVals = "list")[[1]])
RUnit::checkEquals(webquery_res, select_res)
RUnit::checkEquals(webquery_res, select_res2)
ids <- "P06664"
if(online){
webquery <- sprintf("http://www.pantherdb.org/webservices/garuda/search.jsp?keyword=%s&listType=family&type=getList",paste(ids,collapse="+or+"))
res <- read.delim(webquery) # webquery result on 02.02.2021 with v16.0:
dput(sort(as.character(res$Family.Accession)))
}
webquery_res <- c("PTHR10005:SF3", "PTHR10024:SF114", "PTHR10071:SF149", "PTHR10071:SF154",
"PTHR10082:SF28", "PTHR10155:SF3", "PTHR10159:SF309", "PTHR10201:SF24",
"PTHR10218:SF227", "PTHR10218:SF230", "PTHR10218:SF302", "PTHR10218:SF316",
"PTHR10218:SF320", "PTHR10218:SF328", "PTHR10218:SF73", "PTHR10252:SF8",
"PTHR10336:SF12", "PTHR10343:SF84", "PTHR10343:SF89", "PTHR10373:SF25",
"PTHR10373:SF33", "PTHR10378:SF7", "PTHR10502:SF26", "PTHR10522:SF0",
"PTHR10614:SF11", "PTHR10614:SF2", "PTHR10614:SF7", "PTHR10614:SF8",
"PTHR10684:SF3", "PTHR10701:SF3", "PTHR10728:SF13", "PTHR10728:SF39",
"PTHR10827:SF51", "PTHR10844:SF18", "PTHR10913:SF6", "PTHR11042:SF166",
"PTHR11064:SF9", "PTHR11213:SF1", "PTHR11255:SF43", "PTHR11269:SF8",
"PTHR11417:SF5", "PTHR11454:SF9", "PTHR11462:SF37", "PTHR11462:SF7",
"PTHR11462:SF8", "PTHR11509", "PTHR11509:SF0", "PTHR11515:SF11",
"PTHR11515:SF17", "PTHR11544:SF14", "PTHR11566:SF32", "PTHR11584:SF332",
"PTHR11588:SF133", "PTHR11588:SF251", "PTHR11588:SF298", "PTHR11635:SF126",
"PTHR11636:SF47", "PTHR11723:SF16", "PTHR11723:SF5", "PTHR11771:SF33",
"PTHR11801:SF2", "PTHR11848:SF117", "PTHR11848:SF125", "PTHR11848:SF133",
"PTHR11848:SF135", "PTHR11848:SF137", "PTHR11848:SF141", "PTHR11848:SF143",
"PTHR11848:SF165", "PTHR11848:SF22", "PTHR11848:SF29", "PTHR11849:SF178",
"PTHR11850:SF59", "PTHR11850:SF80", "PTHR11850:SF89", "PTHR11866:SF10",
"PTHR11866:SF3", "PTHR11866:SF4", "PTHR11866:SF6", "PTHR11866:SF7",
"PTHR11866:SF8", "PTHR11920:SF494", "PTHR12167:SF2", "PTHR12533:SF11",
"PTHR12533:SF4", "PTHR12533:SF5", "PTHR12533:SF6", "PTHR12623:SF6",
"PTHR12623:SF9", "PTHR12632:SF6", "PTHR13227", "PTHR13227:SF0",
"PTHR13589:SF14", "PTHR13703:SF23", "PTHR13703:SF36", "PTHR13703:SF41",
"PTHR13703:SF42", "PTHR13703:SF45", "PTHR13703:SF53", "PTHR13715:SF51",
"PTHR13715:SF52", "PTHR13715:SF53", "PTHR13780:SF122", "PTHR13780:SF38",
"PTHR13808:SF29", "PTHR13808:SF34", "PTHR13809:SF25", "PTHR13935:SF66",
"PTHR14002:SF7", "PTHR14403", "PTHR14403:SF6", "PTHR15009", "PTHR15009:SF4",
"PTHR15119", "PTHR15119:SF0", "PTHR15359:SF7", "PTHR15427:SF20",
"PTHR15729:SF13", "PTHR18945:SF52", "PTHR19304:SF9", "PTHR19375:SF487",
"PTHR19384:SF63", "PTHR19850:SF27", "PTHR19850:SF28", "PTHR19850:SF29",
"PTHR19850:SF31", "PTHR19850:SF36", "PTHR20855:SF33", "PTHR20855:SF40",
"PTHR22888:SF9", "PTHR23036:SF86", "PTHR23113:SF150", "PTHR23113:SF168",
"PTHR23220:SF22", "PTHR23221", "PTHR23221:SF7", "PTHR23235:SF16",
"PTHR23235:SF42", "PTHR23255:SF22", "PTHR23255:SF49", "PTHR23255:SF50",
"PTHR23255:SF62", "PTHR23255:SF63", "PTHR23255:SF64", "PTHR23255:SF70",
"PTHR23257:SF716", "PTHR23351:SF23", "PTHR23351:SF3", "PTHR23351:SF4",
"PTHR23503:SF51", "PTHR24055:SF107", "PTHR24055:SF109", "PTHR24055:SF110",
"PTHR24055:SF146", "PTHR24055:SF172", "PTHR24055:SF203", "PTHR24055:SF222",
"PTHR24055:SF393", "PTHR24057:SF8", "PTHR24070:SF385", "PTHR24070:SF393",
"PTHR24072:SF105", "PTHR24072:SF136", "PTHR24082:SF197", "PTHR24082:SF488",
"PTHR24085:SF1", "PTHR24086:SF24", "PTHR24139:SF34", "PTHR24169:SF1",
"PTHR24204:SF4", "PTHR24208:SF80", "PTHR24216:SF11", "PTHR24241:SF22",
"PTHR24248:SF87", "PTHR24343:SF306", "PTHR24347:SF403", "PTHR24356:SF158",
"PTHR24356:SF159", "PTHR24356:SF170", "PTHR24356:SF171", "PTHR24356:SF181",
"PTHR24356:SF193", "PTHR24356:SF365", "PTHR24361:SF342", "PTHR24361:SF414",
"PTHR24361:SF656", "PTHR24391:SF17", "PTHR24416:SF106", "PTHR24416:SF535",
"PTHR24416:SF91", "PTHR24418:SF53", "PTHR24418:SF78", "PTHR24418:SF94",
"PTHR44329:SF14", "PTHR44329:SF17", "PTHR44329:SF22", "PTHR44329:SF35",
"PTHR44329:SF39", "PTHR44329:SF46", "PTHR45620:SF12", "PTHR45627:SF26",
"PTHR45628:SF10", "PTHR45628:SF11", "PTHR45628:SF2", "PTHR45628:SF9",
"PTHR45655:SF17", "PTHR45655:SF2", "PTHR45673:SF5", "PTHR45750:SF2",
"PTHR45793:SF9", "PTHR45879:SF1", "PTHR45882:SF1", "PTHR45882:SF4",
"PTHR45976:SF4", "PTHR46037:SF4", "PTHR46180:SF1", "PTHR46385:SF3",
"PTHR46513:SF5", "PTHR46716", "PTHR46716:SF1", "PTHR46845:SF1",
"PTHR48012:SF15", "PTHR48012:SF17", "PTHR48012:SF19", "PTHR48012:SF6",
"PTHR48013:SF12", "PTHR48013:SF17", "PTHR48013:SF21", "PTHR48013:SF23",
"PTHR48013:SF5", "PTHR48013:SF8", "PTHR48015:SF2", "PTHR48016:SF31",
"PTHR48016:SF32", "PTHR48016:SF9", "PTHR48019:SF134", "PTHR48092:SF13",
"PTHR48092:SF15", "PTHR48092:SF5", "PTHR48092:SF6", "PTHR48169:SF1")
# remove non sub family, text search based results, as per above....
webquery_res <- sort(webquery_res[grepl(":",webquery_res)])
select_res <- sort(PANTHER.db::select(PANTHER.db,keys=ids,columns="FAMILY_ID",keytype="PATHWAY_ID")$FAMILY_ID)
RUnit::checkEquals(webquery_res,select_res)
#PANTHER.db::select(PANTHER.db,keys=ids,columns=c( "FAMILY_ID","PATHWAY_ID","SPECIES"),keytype="UNIPROT")
}
test_switch_species <- function(){
#species in PANTHER v16.0
all_specs <- "AMBTC|ANOCA|ANOPHELES|AQUAE|ARABIDOPSIS|ASHGO|ASPFU|BACCR|BACSU|BACTN|BATDJ|BOVINE|BRADI|BRADU|BRAFL|BRANA|BRARP|CAEBR|CANAL|CANINE|CAPAN|CHICKEN|CHIMP|CHLAA|CHLRE|CHLTR|CIOIN|CITSI|CLOBH|COELICOLOR|COXBU|CRYNJ|CUCSA|DAPPU|DEIRA|DICDI|DICPU|DICTD|ECOLI|EMENI|ENTHI|ERYGU|EUCGR|FELCA|FLY|FUSNN|GEOSL|GIAIC|GLOVI|GORGO|GOSHI|HAEIN|HALSA|HELAN|HELPY|HELRO|HORSE|HORVV|HUMAN|IXOSC|JUGRE|KORCO|LACSA|LEIMA|LEPIN|LEPOC|LISMO|MAIZE|MALARIA|MANES|MEDTR|METAC|METJA|MONBE|MONDO|MOUSE|MUSAM|MYCGE|MYCTU|NEIMB|NELNU|NEMVE|NEUCR|NITMS|ORNAN|ORYLA|ORYSJ|OSTTA|PARTE|PHANO|PHODC|PHYPA|PHYRM|PIG|POPTR|PRIPA|PRUPE|PSEAE|PUCGT|PYRAE|RAT|RHESUS|RHOBA|RICCO|SACS2|SALTY|SCHPO|SCLS1|SELML|SETIT|SHEON|SOLLC|SOLTU|SORBI|SOYBN|SPIOL|STAA8|STRPU|STRR6|SYNY3|THAPS|THECC|THEKO|THEMA|THEYD|TOBAC|TRIAD|TRICA|TRIVA|TRYB2|USTMA|VIBCH|VITVI|WHEAT|WORM|XANCP|XENOPUS|YARLI|YEAST|YERPE|ZEBRAFISH|ZOSMR"
RUnit::checkEquals(all_specs,PANTHER.db::pthOrganisms(PANTHER.db))
PANTHER.db::pthOrganisms(PANTHER.db) <- "HUMAN"
RUnit::checkEquals("HUMAN",pthOrganisms(PANTHER.db))
PANTHER.db::resetPthOrganisms(PANTHER.db)
RUnit::checkEquals(all_specs,pthOrganisms(PANTHER.db))
up_out <- c("A0A022RCQ8", "A0A059DAV1", "A0A059DAZ5", "A0A059DBK8", "A0A061ERL3",
"A0A067DRN5", "A0A067DS14", "A0A078FTT2", "A0A090M9A4", "A0A0A0KCA2",
"A0A0D1E928", "A0A0K9PDL1", "A0A0K9R8Y9", "A0A1B6PII2", "A0A1D6KKP7",
"A0A1D6M1W1", "A0A1D8PS33", "A0A1S3X699", "A0A1S4BLA4", "A0A1U8A1J0",
"A0A1U8MP18", "A0A1U8MQ36", "A0A251SF24", "A0A287WKW6", "A0A2C9W1M2",
"A0A2G2ZD67", "A0A2H3ZWF7", "A0A2H3ZXB7", "A0A2I4GKR5", "A0A2I4HVZ7",
"A0A2J6MBB7", "A0A2K1X2L8", "A0A2K1ZTF0", "A0A2K3DMR7", "A0A368RCF8",
"A0A3B6RF57", "A0A3B6SDT6", "A0A3B6TED5", "A0A3Q7HVL1", "A5I427",
"A7ESY6", "A8DW51", "A9A5K6", "A9SBP6", "A9SHU6", "B5YK85", "B6TM42",
"B8C5V3", "B9SUT4", "D7U1M4", "D8QXQ4", "D8SDT9", "F4PCR0", "G7JRL6",
"H3GAG0", "H6QS56", "I1I940", "I1LIK7", "I1LPC2", "K3XG33", "K3ZU56",
"M0RQL3", "M0RR91", "M1CK06", "M4C7X5", "M4CKM3", "M5XDY0", "O25956",
"O59778", "O67104", "P12678", "P12996", "P32451", "P44987", "P53557",
"P54967", "P73538", "P9WPQ7", "Q0TYZ8", "Q2FVJ7", "Q4WD66", "Q58014",
"Q58195", "Q58692", "Q5AYI7", "Q5KEW6", "Q69U93", "Q6C903", "Q74CT7",
"Q7CH65", "Q7NDA8", "Q7RXK2", "Q7UF84", "Q818X3", "Q83CU5", "Q8EDK6",
"Q8F498", "Q8PDF0", "Q8REU0", "Q9AMS7", "Q9FCC3", "Q9I618", "Q9JRW7",
"Q9KSZ4", "U5DC72")
up_all <- sort(select(PANTHER.db,keys="PTHR22976:SF2",keytype="FAMILY_ID",columns="UNIPROT")$UNIPROT)
RUnit::checkEquals(up_out, up_all)
PANTHER.db::pthOrganisms(PANTHER.db) <- "SYNY3"
up_out_syny3 <- "P73538"
up_all_syny3 <- sort(select(PANTHER.db,keys="PTHR22976:SF2",keytype="FAMILY_ID",columns="UNIPROT")$UNIPROT)
RUnit::checkEquals(up_out_syny3, up_all_syny3)
}
ju-mu/PANTHER.db documentation built on March 20, 2021, 10:11 p.m.
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#### Prepare reference queries from PANTHER webservice 18.09.2013 ####
#results will be used for Unit Tests
require(PANTHER.db)
if(F){
library(RCurl)
require(RUnit)
url <- 'http://www.pantherdb.org/webservices/garuda/search.jsp?keyword='
ids <- PANTHER.db::keys(PANTHER.db,"UNIPROT")[c(50,111,444)];ids
fullUrl <- paste0(url,paste(ids[[3]], collapse="|"),'&listType=gene&type=getList')#only one allowed
gs <- read.delim(fullUrl,stringsAsFactors=F)$Gene.Symbol
fullUrl <- paste0(url,paste(ids, collapse="+or+"),'&listType=pathway&type=getList')
path_acc <- read.delim(fullUrl,stringsAsFactors=F)$Pathway.Accession
fullUrl <- paste0(url,paste(ids, collapse="+or+"),'&listType=family&type=getList')
fam_acc <- read.delim(fullUrl,stringsAsFactors=F)$Family.Accession
fullUrl <- paste0(url,paste(ids, collapse="+or+"),'&listType=category&type=getList')
cat_acc <- read.delim(fullUrl,stringsAsFactors=F)$Category.Accession
}
### ###
test_structure <- function(){
RUnit::checkEquals(sort(PANTHER.db::keytypes(PANTHER.db)),sort(PANTHER.db:::.keytypes()))
RUnit::checkEquals(sort(PANTHER.db::keys(PANTHER.db)),sort(PANTHER.db:::.keys(PANTHER.db,"FAMILY_ID")))
RUnit::checkEquals(sort(PANTHER.db::columns(PANTHER.db)),sort(PANTHER.db:::.cols()))
}
online <- FALSE
test_select_vs_webquery <- function(){
ids <- "PTHR10763:SF23"#webserver returns go cats and class ids for all subfamilies
webquery <- sprintf("http://www.pantherdb.org/webservices/garuda/search.jsp?keyword=%s&listType=category&type=getList",ids)
if(online){
res <- read.delim(webquery) #webquery result on 02.02.2021 with v16.0:
dput(sort(as.character(res$Category.Accession)))
}
response.acc <- c("GO:0000075", "GO:0000076", "GO:0000086", "GO:0000228", "GO:0000278",
"GO:0000280", "GO:0000781", "GO:0000784", "GO:0000808", "GO:0003676",
"GO:0003677", "GO:0003688", "GO:0003690", "GO:0005488", "GO:0005622",
"GO:0005634", "GO:0005664", "GO:0005694", "GO:0006139", "GO:0006259",
"GO:0006260", "GO:0006261", "GO:0006270", "GO:0006725", "GO:0006807",
"GO:0006996", "GO:0007049", "GO:0007093", "GO:0007346", "GO:0008152",
"GO:0009058", "GO:0009059", "GO:0009987", "GO:0010389", "GO:0010564",
"GO:0010948", "GO:0010972", "GO:0016043", "GO:0018130", "GO:0019438",
"GO:0022402", "GO:0031570", "GO:0031974", "GO:0031981", "GO:0032991",
"GO:0033314", "GO:0034641", "GO:0034645", "GO:0034654", "GO:0043170",
"GO:0043226", "GO:0043227", "GO:0043228", "GO:0043229", "GO:0043231",
"GO:0043232", "GO:0043233", "GO:0043565", "GO:0044237", "GO:0044238",
"GO:0044249", "GO:0044260", "GO:0044271", "GO:0044770", "GO:0044772",
"GO:0044774", "GO:0044818", "GO:0044839", "GO:0045786", "GO:0045930",
"GO:0046483", "GO:0048285", "GO:0048519", "GO:0048523", "GO:0050789",
"GO:0050794", "GO:0051726", "GO:0065007", "GO:0070013", "GO:0071704",
"GO:0071840", "GO:0071897", "GO:0090304", "GO:0097159", "GO:0098687",
"GO:0110165", "GO:0140014", "GO:1901360", "GO:1901362", "GO:1901363",
"GO:1901576", "GO:1901987", "GO:1901988", "GO:1901990", "GO:1901991",
"GO:1902749", "GO:1902750", "GO:1903047", "GO:1990837", "PC00199")
select_res <- sort( c( PANTHER.db::select(PANTHER.db,keys=ids,columns="GOSLIM_ID")$GOSLIM_ID, PANTHER.db::select(PANTHER.db,keys=ids,columns="CLASS_ID")$CLASS_ID ) )
RUnit::checkEquals(response.acc,select_res)
ids <- "PC00015"
if(online){
webquery <- sprintf("http://www.pantherdb.org/webservices/garuda/search.jsp?keyword=%s&listType=family&type=getList",ids)
res <- read.delim(webquery) # webquery result on 02.02.2021 with v16.0:
dput(sort(as.character(res$Family.Accession)))
}
webquery_res <- c("PTHR11352", "PTHR11352:SF0", "PTHR11352:SF10", "PTHR11352:SF11",
"PTHR11352:SF12", "PTHR11352:SF3", "PTHR11352:SF5", "PTHR11352:SF6",
"PTHR11352:SF8", "PTHR11352:SF9")
select_res <- sort(PANTHER.db::select(PANTHER.db,keys=ids,columns="FAMILY_ID",keytype="CLASS_ID")$FAMILY_ID)
RUnit::checkEquals(webquery_res,select_res)
ids <- "Q90Z00" # PTHR24416:SF131
# DANRE|ZFIN=ZDB-GENE-980526-255|UniProtKB=Q90Z00 Q90Z00 fgfr1a PTHR24416:SF131 TYROSINE-PROTEIN KINASE RECEPTOR
# FGF signaling pathway#P00021>FGFR1-4#P00636;Angiogenesis#P00005>FGFR-1#P00186
if(online){
webquery <- sprintf("http://www.pantherdb.org/webservices/garuda/search.jsp?keyword=%s&listType=pathway&type=getList",paste(ids,collapse="+or+"))
res <- read.delim(webquery) # webquery result on 02.02.2021 with v16.0:
dput(sort(as.character(res$Pathway.Accession)))
}
webquery_res <- c("P00005", "P00021")
# this also returns NA, as there is no Pathway association to Family terms, just to subfamilies!
# BUT:
# From PANTHER authors on 15.10.2019:
# The sequence association file provides direct association of data to the pathway, while keyword search uses rather loose criteria to return results. In your example, the family is an indirect (or inferred) association to the pathway, and thus not included in the sequence association file. The inferred data are allowed in web search or browsing, but not included in any statistical tools. Therefore, they are not included in the sequence association files either.
#
# Hope this helps.
#
# Thanks,
#
# PANTHER feedback
select_res <- sort(PANTHER.db::select(PANTHER.db,keys=ids,columns="PATHWAY_ID",keytype = "UNIPROT")$PATHWAY_ID)
select_res2 <- sort(AnnotationDbi::mapIds(PANTHER.db,keys=ids,column="PATHWAY_ID",keytype="UNIPROT",multiVals = "list")[[1]])
RUnit::checkEquals(webquery_res, select_res)
RUnit::checkEquals(webquery_res, select_res2)
ids <- "P06664"
if(online){
webquery <- sprintf("http://www.pantherdb.org/webservices/garuda/search.jsp?keyword=%s&listType=family&type=getList",paste(ids,collapse="+or+"))
res <- read.delim(webquery) # webquery result on 02.02.2021 with v16.0:
dput(sort(as.character(res$Family.Accession)))
}
webquery_res <- c("PTHR10005:SF3", "PTHR10024:SF114", "PTHR10071:SF149", "PTHR10071:SF154",
"PTHR10082:SF28", "PTHR10155:SF3", "PTHR10159:SF309", "PTHR10201:SF24",
"PTHR10218:SF227", "PTHR10218:SF230", "PTHR10218:SF302", "PTHR10218:SF316",
"PTHR10218:SF320", "PTHR10218:SF328", "PTHR10218:SF73", "PTHR10252:SF8",
"PTHR10336:SF12", "PTHR10343:SF84", "PTHR10343:SF89", "PTHR10373:SF25",
"PTHR10373:SF33", "PTHR10378:SF7", "PTHR10502:SF26", "PTHR10522:SF0",
"PTHR10614:SF11", "PTHR10614:SF2", "PTHR10614:SF7", "PTHR10614:SF8",
"PTHR10684:SF3", "PTHR10701:SF3", "PTHR10728:SF13", "PTHR10728:SF39",
"PTHR10827:SF51", "PTHR10844:SF18", "PTHR10913:SF6", "PTHR11042:SF166",
"PTHR11064:SF9", "PTHR11213:SF1", "PTHR11255:SF43", "PTHR11269:SF8",
"PTHR11417:SF5", "PTHR11454:SF9", "PTHR11462:SF37", "PTHR11462:SF7",
"PTHR11462:SF8", "PTHR11509", "PTHR11509:SF0", "PTHR11515:SF11",
"PTHR11515:SF17", "PTHR11544:SF14", "PTHR11566:SF32", "PTHR11584:SF332",
"PTHR11588:SF133", "PTHR11588:SF251", "PTHR11588:SF298", "PTHR11635:SF126",
"PTHR11636:SF47", "PTHR11723:SF16", "PTHR11723:SF5", "PTHR11771:SF33",
"PTHR11801:SF2", "PTHR11848:SF117", "PTHR11848:SF125", "PTHR11848:SF133",
"PTHR11848:SF135", "PTHR11848:SF137", "PTHR11848:SF141", "PTHR11848:SF143",
"PTHR11848:SF165", "PTHR11848:SF22", "PTHR11848:SF29", "PTHR11849:SF178",
"PTHR11850:SF59", "PTHR11850:SF80", "PTHR11850:SF89", "PTHR11866:SF10",
"PTHR11866:SF3", "PTHR11866:SF4", "PTHR11866:SF6", "PTHR11866:SF7",
"PTHR11866:SF8", "PTHR11920:SF494", "PTHR12167:SF2", "PTHR12533:SF11",
"PTHR12533:SF4", "PTHR12533:SF5", "PTHR12533:SF6", "PTHR12623:SF6",
"PTHR12623:SF9", "PTHR12632:SF6", "PTHR13227", "PTHR13227:SF0",
"PTHR13589:SF14", "PTHR13703:SF23", "PTHR13703:SF36", "PTHR13703:SF41",
"PTHR13703:SF42", "PTHR13703:SF45", "PTHR13703:SF53", "PTHR13715:SF51",
"PTHR13715:SF52", "PTHR13715:SF53", "PTHR13780:SF122", "PTHR13780:SF38",
"PTHR13808:SF29", "PTHR13808:SF34", "PTHR13809:SF25", "PTHR13935:SF66",
"PTHR14002:SF7", "PTHR14403", "PTHR14403:SF6", "PTHR15009", "PTHR15009:SF4",
"PTHR15119", "PTHR15119:SF0", "PTHR15359:SF7", "PTHR15427:SF20",
"PTHR15729:SF13", "PTHR18945:SF52", "PTHR19304:SF9", "PTHR19375:SF487",
"PTHR19384:SF63", "PTHR19850:SF27", "PTHR19850:SF28", "PTHR19850:SF29",
"PTHR19850:SF31", "PTHR19850:SF36", "PTHR20855:SF33", "PTHR20855:SF40",
"PTHR22888:SF9", "PTHR23036:SF86", "PTHR23113:SF150", "PTHR23113:SF168",
"PTHR23220:SF22", "PTHR23221", "PTHR23221:SF7", "PTHR23235:SF16",
"PTHR23235:SF42", "PTHR23255:SF22", "PTHR23255:SF49", "PTHR23255:SF50",
"PTHR23255:SF62", "PTHR23255:SF63", "PTHR23255:SF64", "PTHR23255:SF70",
"PTHR23257:SF716", "PTHR23351:SF23", "PTHR23351:SF3", "PTHR23351:SF4",
"PTHR23503:SF51", "PTHR24055:SF107", "PTHR24055:SF109", "PTHR24055:SF110",
"PTHR24055:SF146", "PTHR24055:SF172", "PTHR24055:SF203", "PTHR24055:SF222",
"PTHR24055:SF393", "PTHR24057:SF8", "PTHR24070:SF385", "PTHR24070:SF393",
"PTHR24072:SF105", "PTHR24072:SF136", "PTHR24082:SF197", "PTHR24082:SF488",
"PTHR24085:SF1", "PTHR24086:SF24", "PTHR24139:SF34", "PTHR24169:SF1",
"PTHR24204:SF4", "PTHR24208:SF80", "PTHR24216:SF11", "PTHR24241:SF22",
"PTHR24248:SF87", "PTHR24343:SF306", "PTHR24347:SF403", "PTHR24356:SF158",
"PTHR24356:SF159", "PTHR24356:SF170", "PTHR24356:SF171", "PTHR24356:SF181",
"PTHR24356:SF193", "PTHR24356:SF365", "PTHR24361:SF342", "PTHR24361:SF414",
"PTHR24361:SF656", "PTHR24391:SF17", "PTHR24416:SF106", "PTHR24416:SF535",
"PTHR24416:SF91", "PTHR24418:SF53", "PTHR24418:SF78", "PTHR24418:SF94",
"PTHR44329:SF14", "PTHR44329:SF17", "PTHR44329:SF22", "PTHR44329:SF35",
"PTHR44329:SF39", "PTHR44329:SF46", "PTHR45620:SF12", "PTHR45627:SF26",
"PTHR45628:SF10", "PTHR45628:SF11", "PTHR45628:SF2", "PTHR45628:SF9",
"PTHR45655:SF17", "PTHR45655:SF2", "PTHR45673:SF5", "PTHR45750:SF2",
"PTHR45793:SF9", "PTHR45879:SF1", "PTHR45882:SF1", "PTHR45882:SF4",
"PTHR45976:SF4", "PTHR46037:SF4", "PTHR46180:SF1", "PTHR46385:SF3",
"PTHR46513:SF5", "PTHR46716", "PTHR46716:SF1", "PTHR46845:SF1",
"PTHR48012:SF15", "PTHR48012:SF17", "PTHR48012:SF19", "PTHR48012:SF6",
"PTHR48013:SF12", "PTHR48013:SF17", "PTHR48013:SF21", "PTHR48013:SF23",
"PTHR48013:SF5", "PTHR48013:SF8", "PTHR48015:SF2", "PTHR48016:SF31",
"PTHR48016:SF32", "PTHR48016:SF9", "PTHR48019:SF134", "PTHR48092:SF13",
"PTHR48092:SF15", "PTHR48092:SF5", "PTHR48092:SF6", "PTHR48169:SF1")
# remove non sub family, text search based results, as per above....
webquery_res <- sort(webquery_res[grepl(":",webquery_res)])
select_res <- sort(PANTHER.db::select(PANTHER.db,keys=ids,columns="FAMILY_ID",keytype="PATHWAY_ID")$FAMILY_ID)
RUnit::checkEquals(webquery_res,select_res)
#PANTHER.db::select(PANTHER.db,keys=ids,columns=c( "FAMILY_ID","PATHWAY_ID","SPECIES"),keytype="UNIPROT")
}
test_switch_species <- function(){
#species in PANTHER v16.0
all_specs <- "AMBTC|ANOCA|ANOPHELES|AQUAE|ARABIDOPSIS|ASHGO|ASPFU|BACCR|BACSU|BACTN|BATDJ|BOVINE|BRADI|BRADU|BRAFL|BRANA|BRARP|CAEBR|CANAL|CANINE|CAPAN|CHICKEN|CHIMP|CHLAA|CHLRE|CHLTR|CIOIN|CITSI|CLOBH|COELICOLOR|COXBU|CRYNJ|CUCSA|DAPPU|DEIRA|DICDI|DICPU|DICTD|ECOLI|EMENI|ENTHI|ERYGU|EUCGR|FELCA|FLY|FUSNN|GEOSL|GIAIC|GLOVI|GORGO|GOSHI|HAEIN|HALSA|HELAN|HELPY|HELRO|HORSE|HORVV|HUMAN|IXOSC|JUGRE|KORCO|LACSA|LEIMA|LEPIN|LEPOC|LISMO|MAIZE|MALARIA|MANES|MEDTR|METAC|METJA|MONBE|MONDO|MOUSE|MUSAM|MYCGE|MYCTU|NEIMB|NELNU|NEMVE|NEUCR|NITMS|ORNAN|ORYLA|ORYSJ|OSTTA|PARTE|PHANO|PHODC|PHYPA|PHYRM|PIG|POPTR|PRIPA|PRUPE|PSEAE|PUCGT|PYRAE|RAT|RHESUS|RHOBA|RICCO|SACS2|SALTY|SCHPO|SCLS1|SELML|SETIT|SHEON|SOLLC|SOLTU|SORBI|SOYBN|SPIOL|STAA8|STRPU|STRR6|SYNY3|THAPS|THECC|THEKO|THEMA|THEYD|TOBAC|TRIAD|TRICA|TRIVA|TRYB2|USTMA|VIBCH|VITVI|WHEAT|WORM|XANCP|XENOPUS|YARLI|YEAST|YERPE|ZEBRAFISH|ZOSMR"
RUnit::checkEquals(all_specs,PANTHER.db::pthOrganisms(PANTHER.db))
PANTHER.db::pthOrganisms(PANTHER.db) <- "HUMAN"
RUnit::checkEquals("HUMAN",pthOrganisms(PANTHER.db))
PANTHER.db::resetPthOrganisms(PANTHER.db)
RUnit::checkEquals(all_specs,pthOrganisms(PANTHER.db))
up_out <- c("A0A022RCQ8", "A0A059DAV1", "A0A059DAZ5", "A0A059DBK8", "A0A061ERL3",
"A0A067DRN5", "A0A067DS14", "A0A078FTT2", "A0A090M9A4", "A0A0A0KCA2",
"A0A0D1E928", "A0A0K9PDL1", "A0A0K9R8Y9", "A0A1B6PII2", "A0A1D6KKP7",
"A0A1D6M1W1", "A0A1D8PS33", "A0A1S3X699", "A0A1S4BLA4", "A0A1U8A1J0",
"A0A1U8MP18", "A0A1U8MQ36", "A0A251SF24", "A0A287WKW6", "A0A2C9W1M2",
"A0A2G2ZD67", "A0A2H3ZWF7", "A0A2H3ZXB7", "A0A2I4GKR5", "A0A2I4HVZ7",
"A0A2J6MBB7", "A0A2K1X2L8", "A0A2K1ZTF0", "A0A2K3DMR7", "A0A368RCF8",
"A0A3B6RF57", "A0A3B6SDT6", "A0A3B6TED5", "A0A3Q7HVL1", "A5I427",
"A7ESY6", "A8DW51", "A9A5K6", "A9SBP6", "A9SHU6", "B5YK85", "B6TM42",
"B8C5V3", "B9SUT4", "D7U1M4", "D8QXQ4", "D8SDT9", "F4PCR0", "G7JRL6",
"H3GAG0", "H6QS56", "I1I940", "I1LIK7", "I1LPC2", "K3XG33", "K3ZU56",
"M0RQL3", "M0RR91", "M1CK06", "M4C7X5", "M4CKM3", "M5XDY0", "O25956",
"O59778", "O67104", "P12678", "P12996", "P32451", "P44987", "P53557",
"P54967", "P73538", "P9WPQ7", "Q0TYZ8", "Q2FVJ7", "Q4WD66", "Q58014",
"Q58195", "Q58692", "Q5AYI7", "Q5KEW6", "Q69U93", "Q6C903", "Q74CT7",
"Q7CH65", "Q7NDA8", "Q7RXK2", "Q7UF84", "Q818X3", "Q83CU5", "Q8EDK6",
"Q8F498", "Q8PDF0", "Q8REU0", "Q9AMS7", "Q9FCC3", "Q9I618", "Q9JRW7",
"Q9KSZ4", "U5DC72")
up_all <- sort(select(PANTHER.db,keys="PTHR22976:SF2",keytype="FAMILY_ID",columns="UNIPROT")$UNIPROT)
RUnit::checkEquals(up_out, up_all)
PANTHER.db::pthOrganisms(PANTHER.db) <- "SYNY3"
up_out_syny3 <- "P73538"
up_all_syny3 <- sort(select(PANTHER.db,keys="PTHR22976:SF2",keytype="FAMILY_ID",columns="UNIPROT")$UNIPROT)
RUnit::checkEquals(up_out_syny3, up_all_syny3)
}
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