dataInput {SDAMS} | R Documentation |
Two ways to input metabolomics or proteomics data from mass spectrometry as
SummarizedExperiment
:
createSEFromCSV
creates SummarizedExperiment object from csv files;
createSEFromMatrix
creates SummarizedExperiment object from
separate matrices: one for feature data and the other one for colData.
createSEFromCSV(featurePath, colDataPath, rownames1 = 1, rownames2 = 1, header1 = TRUE, header2 = TRUE) createSEFromMatrix(feature, colData)
featurePath |
path for feature data. |
colDataPath |
path for colData. |
rownames1 |
indicator for feature data with row names. If NULL, row numbers are automatically generated. |
rownames2 |
indicator for colData with row names. If NULL, row numbers are automatically generated. |
header1 |
a logical value indicating whether the first row of feature is column names. The default value is TRUE. |
header2 |
a logical value indicating whether the first row of colData is column names. The default value is TRUE. If colData input is a vector, set to False. |
feature |
a matrix with row being features and column being subjects. |
colData |
a column type data containing information about the subjects. |
An object of SummarizedExperiment
class.
Yuntong Li <yuntong.li@uky.edu>, Chi Wang <chi.wang@uky.edu>, Li Chen <lichenuky@uky.edu>
SDA
input requires an object of SummarizedExperiment
class.
# ---------- csv input ------------- directory1 <- system.file("extdata", package = "SDAMS", mustWork = TRUE) path1 <- file.path(directory1, "ProstateFeature.csv") directory2 <- system.file("extdata", package = "SDAMS", mustWork = TRUE) path2 <- file.path(directory2, "ProstateGroup.csv") exampleSE <- createSEFromCSV(path1, path2) exampleSE # ---------- matrix input ------------- set.seed(100) featureInfo <- matrix(runif(800, -2, 5), ncol = 40) featureInfo[featureInfo<0] <- 0 rownames(featureInfo) <- paste("feature", 1:20, sep = '') colnames(featureInfo) <- paste('subject', 1:40, sep = '') groupInfo <- data.frame(grouping=matrix(sample(0:1, 40, replace = TRUE), ncol = 1)) rownames(groupInfo) <- colnames(featureInfo) exampleSE <- createSEFromMatrix(feature = featureInfo, colData = groupInfo) exampleSE