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Update write_dgCMatrix_csv #31

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Update write_dgCMatrix_csv #31

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14 changes: 8 additions & 6 deletions R/write_csv.R
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Original file line number Diff line number Diff line change
Expand Up @@ -28,6 +28,7 @@ write_dgCMatrix_csv <- function(mat,
n_row <- length(row_names)
n_col <- length(col_names)

chunk_size = min(chunk_size, n_row)
n_chunks <- floor(n_row/chunk_size)

# Initial chunk
Expand All @@ -41,7 +42,7 @@ write_dgCMatrix_csv <- function(mat,
data.table::fwrite(chunk_df, file = filename, append = F)

# chunkation over chunks
for(chunk in 2:n_chunks) {
for(chunk in seq(n_chunks)[-1]) {
chunk_start <- 1 + chunk_size * (chunk - 1)
chunk_end <- chunk_size * chunk
print(paste0("Writing rows ",chunk_start," to ", chunk_end))
Expand All @@ -53,9 +54,10 @@ write_dgCMatrix_csv <- function(mat,
# Remaining samples
chunk_start <- (n_chunks*chunk_size + 1)
chunk_end <- n_row
print(paste0("Writing rows ",chunk_start," to ", chunk_end))
chunk_mat <- t(as.matrix(mat[,chunk_start:chunk_end]))
chunk_df <- cbind(data.frame(col1 = row_names[chunk_start:chunk_end]),as.data.frame(chunk_mat))
data.table::fwrite(chunk_df, file = filename, append = T)

if (chunk_start < chunk_end) {
print(paste0("Writing rows ",chunk_start," to ", chunk_end))
chunk_mat <- t(as.matrix(mat[,chunk_start:chunk_end]))
chunk_df <- cbind(data.frame(col1 = row_names[chunk_start:chunk_end]),as.data.frame(chunk_mat))
data.table::fwrite(chunk_df, file = filename, append = T)
}
}