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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,14 +1,16 @@ | ||
| Package: NanoStringNorm | ||
| Type: Package | ||
| Title: Normalize NanoString miRNA and mRNA Data | ||
| Version: 2.0.0 | ||
| Date: 2023-03-21 | ||
| Version: 3.0.0 | ||
| Date: 2025-01-15 | ||
| Authors@R: c( | ||
| person(c("Daryl", "M."), "Waggott", role = "aut"), | ||
| person("Paul", "Boutros", email = "[email protected]", role = "cre"), | ||
| person("Dan", "Knight", role = "ctb")) | ||
| Depends: R (>= 2.14.0), gdata (>= 2.8.2), XML (>= 3.98-1.5) | ||
| Imports: methods | ||
| Depends: | ||
| R (>= 2.14.0) | ||
| Imports: | ||
| methods | ||
| Suggests: googleVis (>= 0.2.14), lme4, RUnit (>= 0.4.26) | ||
| Description: A set of tools for normalizing, diagnostics and visualization of NanoString nCounter data. | ||
| License: GPL-2 | ||
|
|
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,84 @@ | ||
| read.csv.RCC <- function(path, sample.id.row = 'File.Name') { | ||
| if (!file.exists(path)) { | ||
| stop(paste('File not found:', path)) ; | ||
| } | ||
|
|
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| prep.rcc <- function(path) { | ||
| data <- read.csv( | ||
| path, | ||
| header = FALSE, | ||
| strip.white = TRUE | ||
| ); | ||
| data <- data[!sapply(data, function(x) all(is.na(x)))]; | ||
|
|
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| data.start.index <- min(which(data[, 1] == 'Reporter Counts')); | ||
| header <- data[1:(data.start.index - 1), ]; | ||
| data <- data[data.start.index:nrow(data), ]; | ||
|
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| return(list( | ||
| header = header, | ||
| x = data | ||
| )); | ||
| } | ||
| rcc <- prep.rcc(path); | ||
|
|
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| if (is.null(rcc$header)) { | ||
| stop('There appears to be a problem with the RCC CSV file. No header information found.'); | ||
| } | ||
|
|
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| rcc$header <- rcc$header[is.na(rcc$header[1]) | (rcc$header[1] != ''), ]; | ||
| rownames(rcc$header) <- rcc$header[, 1]; | ||
| rcc$header <- rcc$header[, -1]; | ||
|
|
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| rownames(rcc$header) <- gsub(' $', '', rownames(rcc$header)); | ||
| rownames(rcc$header) <- gsub(' ', '.', rownames(rcc$header)); | ||
| rownames(rcc$header) <- tolower(rownames(rcc$header)); | ||
|
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| if ('id' %in% rownames(rcc$header)) { | ||
| rownames(rcc$header)[rownames(rcc$header) == 'id'] <- 'sample.id'; | ||
| } | ||
|
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| if (!all(c('file.name', 'sample.id', 'binding.density') %in% rownames(rcc$header))) { | ||
| stop('There appears to be a problem with the RCC CSV file. Rownames in header are missing "File name", "Sample id", "Binding density"'); | ||
| } | ||
|
|
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| rcc$header <- rcc$header[!rownames(rcc$header) %in% c('file.attributes', 'lane.attributes'), -c(1,2)]; | ||
|
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| sample.ids <- rcc$header[rownames(rcc$header) %in% tolower(sample.id.row),]; | ||
| sample.ids <- gsub(' ', '.', sample.ids); | ||
| sample.ids <- gsub('^([0-9])', 'X\\1', sample.ids); | ||
| colnames(rcc$header) <- sample.ids; | ||
|
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| if (is.null(rcc$x)) { | ||
| stop('There appears to be a problem with the RCC CSV file. Likely couldnt find the count specifically "Code Class" in header information.'); | ||
| } | ||
|
|
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| colnames(rcc$x) <- rcc$x[2, ]; | ||
| rcc$x <- rcc$x[-c(1:2), 1:(3 + length(sample.ids))]; | ||
|
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| rows.with.missing.anno <- (rcc$x[, 1] == '' | rcc$x[, 2] == ''); | ||
| if (any(rows.with.missing.anno)) { | ||
| rcc$x <- rcc$x[!rows.with.missing.anno,]; | ||
| cat(paste('The following row(s)', paste(which(rows.with.missing.anno), collapse = ', '), 'have been dropped due to missing annotation.\n\t You may want to double check the excel file.\n\n')); | ||
| } | ||
|
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| colnames(rcc$x) <- gsub(' ', '.', colnames(rcc$x)); | ||
| colnames(rcc$x) <- c(colnames(rcc$x)[1:3], sample.ids); | ||
|
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| cat(paste('There were', length(sample.ids), 'samples imported. \nNote that spaces in sample names will be replaced by dots. \n')); | ||
|
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| if (length(sample.ids) > 5) { | ||
| cat('The first and last 3 sample names found in the dataset are:\n'); | ||
| cat(paste(c(sample.ids[1:3], rev(sample.ids)[1:3]))); | ||
| } | ||
| else { | ||
| cat('The sample names found in the dataset are:\n'); | ||
| cat(paste(sample.ids)); | ||
| } | ||
|
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| cat(paste('\n\nThere were', nrow(rcc$x), 'genes imported with the following Code Class breakdown:')); | ||
| print(table(rcc$x[, 'Code.Class'])); | ||
|
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| class(rcc) <- 'NanoString'; | ||
| return(rcc); | ||
| } |
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