metaSeq (version 1.12.0)

meta.readData: readData function for meta-analysis

Description

readData function in NOISeq package customized for one-sided test in meta-analysis. Parallel computing is also available by snow package.

Usage

meta.readData(data = NULL, factors = NULL, length = NULL, biotype = NULL, chromosome = NULL, gc = NULL, studies = NULL)

Arguments

data

Matrix or data.frame containing the counts (or expression data) for each feature and sample. Features must be in rows and samples must be in columns.

factors

A data.frame containing the experimental condition or group for each sample (columns in the data object).

length

Optional argument.Vector, matrix or data.frame containing the length of each feature. In case of giving a vector, the names of the vector must be the feature names or ids with the same type of identifier used in data. If a matrix or a data.frame is provided, and it has two columns, it is expected that the feature names or ids are in the first column and the length of the features in the second. If it only has one column containing the length, the rownames of the object must be the feature names or ids.

biotype

Optional argument.Vector, matrix or data.frame containing the biological group (biotype) for each feature. In case of giving a vector, the names of the vector must be the feature names or ids with the same type of identifier used in data. If a matrix or a data.frame is provided, and it has two columns, it is expected that the feature names or ids are in the first column and the biotypes of the features in the second. If it only has one column containing the biotypes, the rownames of the object must be the feature names or ids.

chromosome

Optional argument. A matrix or data.frame containing the chromosome, start position and end position of each feature. The rownames must be the feature names or ids with the same type of identifier used in data.

gc

Optional argument.Vector, matrix or data.frame containing the GC content of each feature. In case of giving a vector, the names of the vector must be the feature names or ids with the same type of identifier used in data. If a matrix or a data.frame is provided, and it has two columns, it is expected that the feature names or ids are in the first column and the GC content of the features in the second. If it only has one column containing the GC content, the rownames of the object must be the feature names or ids.

studies

A vector specifying which column in data are measured in common study. Its length must be equal to the number of column in data.

References

Tarazona, S. and Garcia-Alcalde, F. and Dopazo, J. and Ferrer, A. and Conesa, A. (2011) Differential expression in RNA-seq: A matter of depth. Genome Research, 21(12): 2213-2223

See Also

readData

Examples

data(BreastCancer)
library("snow")

# Experimental condition (1: BreastCancer, 0: Normal)
flag1 <- c(1,1,1,0,0, 1,0, 1,1,1,1,1,1,1,0, 1,1,0)

# Source of data
flag2 <- c("A","A","A","A","A", "B","B", "C","C","C","C","C","C","C","C", "D","D","D")

# readData function for meta-analysis
cds <- meta.readData(data = BreastCancer, factor = flag1, studies = flag2)

# oneside NOISeq for meta-analysis
# cl <- makeCluster(4, "SOCK")
# result <- meta.oneside.noiseq(cds, k = 0.5, norm = "tmm", replicates = "biological", factor = flag1, conditions = c(1, 0), studies = flag2, cl = cl)
# stopCluster(cl)

# Script above is very time-consumming step. Please use this pre-calculated result instead
data(Result.Meta)
result <- Result.Meta

# Fisher's method (without weighting)
F <- Fisher.test(result)
str(F)

# Stouffer's method (with weighting by sample-size)
S <- Stouffer.test(result)
str(S)