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1 minor change and 1 critical change #13

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1 minor change and 1 critical change #13

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7715084
Remove the request for writing to harddrive
ETaSky Jan 31, 2020
d7ddd8d
Fix the problem with unknown_initialize_1
ETaSky Jan 31, 2020
342b9c4
Small fix 1 in FEAST_rarefy
ETaSky Oct 9, 2020
a6b4411
edit the unkown_intialize_1 function
ETaSky Oct 15, 2020
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9 changes: 5 additions & 4 deletions R/FEAST.R
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Original file line number Diff line number Diff line change
Expand Up @@ -41,8 +41,7 @@
#' }
#'
#' @export
FEAST <- function(C, metadata, EM_iterations = 1000, COVERAGE = NULL ,different_sources_flag,
dir_path, outfile){
FEAST <- function(C, metadata, EM_iterations = 1000, COVERAGE = NULL ,different_sources_flag, dir_path = NULL, outfile = NULL){

###1. Parse metadata and check it has the correct hearer (i.e., Env, SourceSink, id)
if(sum(colnames(metadata)=='Env')==0) stop("The metadata file must contain an 'Env' column naming the source environment for each sample.")
Expand Down Expand Up @@ -143,9 +142,11 @@ FEAST <- function(C, metadata, EM_iterations = 1000, COVERAGE = NULL ,different_
colnames(proportions_mat) <- c(envs_sources, "Unknown")
rownames(proportions_mat) <- envs_sink
# proportions_mat[is.na(proportions_mat)] <- 999
if(!is.null(dir_path)){
setwd(dir_path)
write.table(proportions_mat, file = paste0(outfile,"_source_contributions_matrix.txt"), sep = "\t")
}

setwd(dir_path)
write.table(proportions_mat, file = paste0(outfile,"_source_contributions_matrix.txt"), sep = "\t")
return(proportions_mat)

}
3 changes: 1 addition & 2 deletions R/Infer_LatentVariables.R
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Expand Up @@ -129,7 +129,6 @@ unknown_initialize_1 <- function(sources, sink, n_sources){
sources_sum <- apply(sources, 2 ,sum)


unknown_source <- c()

if(n_sources > 1){

Expand Down Expand Up @@ -169,7 +168,7 @@ unknown_initialize_1 <- function(sources, sink, n_sources){
if(length(ind_cor_all) > 1){

cor_abundance <- round(apply(sources[,ind_cor_all], 2, min)/2) #take the min abundnace of the 'cor'
unknown_source[ind_cor_all] <- 0
unknown_source[ind_cor_all] <- cor_abundance


}
Expand Down
2 changes: 1 addition & 1 deletion R/utils.R
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Expand Up @@ -44,7 +44,7 @@ FEAST_rarefy <- function(x,maxdepth){

if(is.null(maxdepth)) return(x)

if(!is.element(class(x), c('matrix', 'data.frame','array')))
if(!any(is.element(class(x), c('matrix', 'data.frame','array'))))
x <- matrix(x,nrow=nrow(x))
nr <- nrow(x)
nc <- ncol(x)
Expand Down