readExpData: Read in expression data
In gage: Generally Applicable Gene-set Enrichment for Pathway Analysis

Description Usage Arguments Details Value Author(s) References See Also Examples

This is a wrapper function of read.delim for reading in expression data matrix in tab-delimited format.

1	readExpData(file = "arrayData.txt", ...)

`file`	character string, the full path name to the expression data file in tab-delimited format. Rows are genes, columns are array samples.
`...`	other arguments to be passed into `read.delim` function.

readExpData is a wrapper function of read.delim. Please check help information of read.delim for more details.

A data.frame (matrix-like) of gene expression data. Rows are genes, columns are array samples.

Weijun Luo <luo_weijun@yahoo.com>

Luo, W., Friedman, M., Shedden K., Hankenson, K. and Woolf, P GAGE: Generally Applicable Gene Set Enrichment for Pathways Analysis. BMC Bioinformatics 2009, 10:161

readList read in gene set list

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filename=system.file("extdata/gse16873.demo", package = "gage")
demo.data=readExpData(filename, row.names=1)
head(demo.data)

              HN_1   DCIS_1     HN_2   DCIS_2     HN_3   DCIS_3     HN_4
10000     6.765984 6.458339 6.921720 6.774493 7.010564 6.986779 6.958761
10001     6.339474 6.755342 7.177369 6.842597 7.392611 6.879474 6.296571
10002     6.591755 6.790304 6.735359 6.773255 6.700016 7.041881 6.586285
10003     6.822092 6.590539 6.508452 6.411859 6.575640 6.470913 6.896886
100048912 7.356051 7.311144 7.385513 7.333481 7.392233 7.428623 7.314579
10004     6.941935 6.854373 6.883973 6.833695 6.855043 6.856864 7.021072
            DCIS_4     HN_5   DCIS_5     HN_6   DCIS_6
10000     6.888199 6.949912 6.948589 7.220427 7.070159
10001     6.130034 7.831222 7.942344 7.665248 7.799255
10002     6.501011 6.884931 7.652490 7.342505 7.500791
10003     6.848872 6.615143 6.407087 6.618174 6.651619
100048912 7.362658 7.370044 7.397249 7.383196 7.437643
10004     7.051310 6.767242 6.775276 6.873855 6.805247