NEWS

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SimSeq 1.4.0 (2015-11-23)

• Updated maintainer address

SimSeq 1.3.0 (2015-03-07)

• Added citation file
• Added SimSeq paper to sources of SimData function
• Added gene annotations to KIRC dataset
• Add in vector of DE genes to output of SimData function

SimSeq 1.2.0 (2014-12-10)

• Set default norm factors estimation to 0.75 quantile of all counts
• Removed edgeR dependency
• Added in full TCGA KIRC dataset version 1.5.0
• Added in switch to change factor levels (treatment groups) around in SimData function
• Updated documentations files

SimSeq 1.1.0

• Updated SimData function to return columns used in sampling algorithm

SimSeq 1.0.0 (2014-02-18)

• Initial CRAN release

SimSeq 0.5.2

• Updated package namespace to export and import variables
• Changed depends to imports for edgeR and fdrtool
• Fixed treatment output in function SimData
• Removed algorithm from documentation for function SimData
• Removed samp.col from output for function SimData
• Changed treatment from 0 and 1 to non-tumor and tumor in kidney dataset

SimSeq 0.5.1

• fixed bug in samp.independent method in SimData function when samp.independent equal TRUE
• updated documentation

SimSeq 0.5.0

• changed name of "offset" input to "norm.factors" in all functions
• removed symmetric swapping functionally. As such n1.diff, n1.genes, and genes1.select are removed from all functions
• Updated Documentation
• Moved packages 'edgeR' and 'fdrtool's back to Depends field
• updated demo file

SimSeq 0.4.0

• Changed version names of all files from 1.x.y to 0.x.y
• removed pval.hist function
• now calculates weights for sampling genes by local fdr through fdrtool function from CRAN package 'fdrtool'
• changed name of EBP input in SimData function to weights
• updated examples for SimData
• updated documentation of functions
• removed package 'edgeR' from Depends field in description file
• added package 'edgeR' and 'fdrtool' to Suggests field in description file

SimSeq 0.3.0

• Moved wilcox signed rank and rank sum test out of SimData function to its own function, CalcPvalWilcox
• Changed default for offsets to calcNormFactors from package 'edgeR' using method "TMM"
• Created dependency on package 'edgeR'
• Changed independence swapping code (changed method for adjusting data by offsets, eliminated for-loops)
• Set samp.independent default to FALSE
• Minimal cleaning up of help/documentation files (still needs a bit of work)
• Created CalcPvalWilcox .Rd file

SimSeq 0.2.0

• Substantially cleaned up code for readability and maintainability
• Added more detailed comments to code
• Renamed data.sim and sortdata functions to SimData and SortData respectively
• Added samp.genes functions
• Fixed errors in offset under the independent method section

SimSeq 0.1.0

• Added symmetric swap functionality to data.sim function
• Added checks on initial parameters submitted to data.sim function
• help files are no longer working

SimSeq 0.0.0

• Created sortdata, samp.col, and data.sim functions
• sortdata: sorts matrix of gene express. data given vector of replicates and treatment
• samp.col: samples replicates by columns separately and independently
• data.sim: Now has functionality to simulate under both standard and independent method for both paired and unpaired data