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Merge branch 'baps-file' into issue-2-greedy-test

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This commit is contained in:
Waldir Leoncio 2021-03-30 08:23:44 +02:00
commit 2bb94b815c
3 changed files with 7 additions and 7 deletions
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4
R/greedyMix.R
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@ -68,14 +68,14 @@ greedyMix <- function(
# fprintf(1,'Data: %s\n',[pathname filename]); # fprintf(1,'Data: %s\n',[pathname filename]);
# end # end
data <- read.delim(pathname_filename) # TODO: discover delimiter data <- read.delim(pathname_filename, header = FALSE, sep = " ")
ninds <- testaaOnkoKunnollinenBapsData(data) # testing ninds <- testaaOnkoKunnollinenBapsData(data) # testing
if (ninds == 0) stop('Incorrect Data-file') if (ninds == 0) stop('Incorrect Data-file')
# ASK: remove? # ASK: remove?
# h0 = findobj('Tag','filename1_text'); # h0 = findobj('Tag','filename1_text');
# set(h0,'String',filename); clear h0; # set(h0,'String',filename); clear h0;
cat( message(
'When using data which are in BAPS-format,', 'When using data which are in BAPS-format,',
'you can specify the sampling populations of the', 'you can specify the sampling populations of the',
'individuals by giving two additional files:', 'individuals by giving two additional files:',

4
R/testaaOnkoKunnollinenBapsData.R
View file

@ -7,13 +7,13 @@ testaaOnkoKunnollinenBapsData <- function(data) {
# Tarkastaa onko viimeisess?sarakkeessa kaikki # Tarkastaa onko viimeisess?sarakkeessa kaikki
# luvut 1,2,...,n johonkin n:<3A><>n asti. # luvut 1,2,...,n johonkin n:<3A><>n asti.
# Tarkastaa lis<69>ksi, ett?on v<>hint<6E><74>n 2 saraketta. # Tarkastaa lis<69>ksi, ett?on v<>hint<6E><74>n 2 saraketta.
if (size[data, 1] < 2) { if (size(data, 1) < 2) {
ninds <- 0 ninds <- 0
return(ninds) return(ninds)
} }
lastCol <- data[, ncol(data)] lastCol <- data[, ncol(data)]
ninds <- max(lastCol) ninds <- max(lastCol)
if (t(1:ninds) != unique(lastCol)) { if (any(1:ninds != unique(lastCol))) {
ninds <- 0 ninds <- 0
return(ninds) return(ninds)
} }

4
tests/testthat/test-greedyMix.R
View file

@ -2,8 +2,8 @@ context("Opening files on greedyMix")
# TODO: needs #12 to be fixed before this can be done without user intervention # TODO: needs #12 to be fixed before this can be done without user intervention
greedyMix( greedyMix(
tietue = "inst/ext/ExamplesDataFormatting/Example baseline data in GENEPOP format for Trained clustering.txt", tietue = "inst/ext/ExamplesDataFormatting/Example data in BAPS format for clustering of diploid individuals.txt",
format = "GenePop", format = "BAPS",
savePreProcessed = FALSE savePreProcessed = FALSE
) # Upper bounds 100 100 ) # Upper bounds 100 100