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Update in User Guide/User Input.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/DEsubs@123204 bc3139a8-67e5-0310-9ffc-ced21a209358

Aristidis G Vrahatis authored on 31/10/2016 15:11:03
Showing 3 changed files

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 Package: DEsubs
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-Version: 1.1.0
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+Version: 1.1.1
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 Date: 2015-07-19
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 Title: DEsubs: an R package for flexible identification of
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         differentially expressed subpathways using RNA-seq expression
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\ No newline at end of file
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+1.1.1: - Update in User Guide/User Input
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+
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+1.1.0: - Initial version
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\ No newline at end of file
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@@ -58,7 +58,7 @@ if (.Platform[['OS.type']] == 'windows')
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 }
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 ```
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-Now the packake, as well as the toy-data can be loaded as follows:
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+Now the package, as well as the toy-data can be loaded as follows:
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 ```{r eval=FALSE, echo=TRUE}
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 library('DEsubs')
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@@ -88,7 +88,7 @@ load(system.file('extdata', 'data.RData', package='DEsubs'))
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 \newpage
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 ## 2. User Input
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-DEsubs accepts RNA-seq expression control-case profile data. The following 
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+DEsubs accepts RNA-seq expression paired case-control profile data. The following 
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 example in Table 1 shows the right structure for RNA-seq expression data input.
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@@ -103,7 +103,7 @@ data <- c(    1879, 2734, 2369, 2636, 2188, 9743, 9932, 10099,
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 data <- matrix(data, nrow=6, ncol=8, byrow=TRUE)
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 rownames(data) <- c(paste0('Gene ', 1:3), '...',  'Gene N-1', 'Gene N')
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-colnames(data) <- paste0('Sample ', 1:8)
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+colnames(data) <- c(paste0('Case ', 1:4), paste0('Control ', 1:4))
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 kable( data,
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     caption = 'Example of user input format' )