Description Usage Arguments Value Author(s) References See Also Examples
This function normalizes sequencing count data. It accepts the count matrix and sample metadata (optional) in form of SummarizedExperiment
or data.frame
. In either class, the columns and rows of the count matix should be sample/conditions and genes respectively.
1 |
data |
An object of |
norm.fun |
One of the normalizing functions: "CNF", "ESF", "VST", "rlog". Specifically, "CNF" stands for |
parameter.list |
A list of parameters for each normalizing function assigned in |
data.trans |
One of "log2", "exp2", and "none", corresponding to transform the count matrix by "log2", "2-based exponent", and "no transformation" respecitvely. The default is "none". |
If the input data is SummarizedExperiment
, the retured value is also a SummarizedExperiment
containing normalized data matrix and metadata (optional). If the input data is a data.frame
, the returned value is a data.frame
of normalized data and metadata (optional).
Jianhai Zhang jzhan067@ucr.edu; zhang.jianhai@hotmail.com
Dr. Thomas Girke thomas.girke@ucr.edu
SummarizedExperiment: SummarizedExperiment container. R package version 1.10.1
R Core Team (2018). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL https://www.R-project.org/
McCarthy, Davis J., Chen, Yunshun, Smyth, and Gordon K. 2012. "Differential Expression Analysis of Multifactor RNA-Seq Experiments with Respect to Biological Variation." Nucleic Acids Research 40 (10): 4288–97
Keays, Maria. 2019. ExpressionAtlas: Download Datasets from EMBL-EBI Expression Atlas
Love, Michael I., Wolfgang Huber, and Simon Anders. 2014. "Moderated Estimation of Fold Change and Dispersion for RNA-Seq Data with DESeq2." Genome Biology 15 (12): 550. doi:10.1186/s13059-014-0550-8
McCarthy, Davis J., Chen, Yunshun, Smyth, and Gordon K. 2012. "Differential Expression Analysis of Multifactor RNA-Seq Experiments with Respect to Biological Variation." Nucleic Acids Research 40 (10): 4288–97
Cardoso-Moreira, Margarida, Jean Halbert, Delphine Valloton, Britta Velten, Chunyan Chen, Yi Shao, Angélica Liechti, et al. 2019. “Gene Expression Across Mammalian Organ Development.” Nature 571 (7766): 505–9
calcNormFactors
in edgeR, and estimateSizeFactors
, varianceStabilizingTransformation
, rlog
in DESeq2.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 | ## In the following examples, the 2 toy data come from an RNA-seq analysis on development of 7
## chicken organs under 9 time points (Cardoso-Moreira et al. 2019). For conveninece, they are
## included in this package. The complete raw count data are downloaded using the R package
## ExpressionAtlas (Keays 2019) with the accession number "E-MTAB-6769". Toy data1 is used as
## a "data frame" input to exemplify data of simple samples/conditions, while toy data2 as
## "SummarizedExperiment" to illustrate data involving complex samples/conditions.
## Set up toy data.
# Access toy data1.
cnt.chk.simple <- system.file('extdata/shinyApp/example/count_chicken_simple.txt',
package='spatialHeatmap')
df.chk <- read.table(cnt.chk.simple, header=TRUE, row.names=1, sep='\t', check.names=FALSE)
# Columns follow the namig scheme "sample__condition", where "sample" and "condition" stands
# for organs and time points respectively.
df.chk[1:3, ]
# A column of gene annotation can be appended to the data frame, but is not required.
ann <- paste0('ann', seq_len(nrow(df.chk))); ann[1:3]
df.chk <- cbind(df.chk, ann=ann)
df.chk[1:3, ]
# Access toy data2.
cnt.chk <- system.file('extdata/shinyApp/example/count_chicken.txt', package='spatialHeatmap')
count.chk <- read.table(cnt.chk, header=TRUE, row.names=1, sep='\t')
count.chk[1:3, 1:5]
# Store toy data2 in "SummarizedExperiment".
library(SummarizedExperiment)
se.chk <- SummarizedExperiment(assay=count.chk)
# Normalize raw count data. The normalizing function "calcNormFactors" (McCarthy et al. 2012)
# with default settings is used.
df.nor.chk <- norm_data(data=df.chk, norm.fun='CNF', data.trans='log2')
se.nor.chk <- norm_data(data=se.chk, norm.fun='CNF', data.trans='log2')
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.