NEWS.md

In RGLab/flowCore: flowCore: Basic structures for flow cytometry data

flowCore 1.15.2

• Modified the logicle and the inverse logicle transformation to make use of the C++ library provided by Wayne Moore et al.

• Added a function estimateLogicle to automatically estimate the logicle transformation parameters given a flowFrame and the channels to be transformed as input.

• Modified the inverseLogicleTransfom function to take the output of a logicleTransform function as input.

flowCore 1.21.1

• add TEXT segment parser in readFCStext function for FCS3 when the delimiter characters existing inside of keyword values. Note this parser require all keywords and their values to be non-empty, which conforms to FCS3 standard

flowCore 1.21.5

• add .readFCSdataRaw routine to read FCS containing bit-packed integer data (with odd-bitwidth like 9,11 instead of 8,16,32,64) .Currently the bit-wise manipulation is done within R,it can be moved to C if speed issue becomes a problem in the future.

flowCore 1.23.2

• add new classes "filters", "filtersList" to allow flowViz to plot multiple filters/gates for one flowFrame

flowCore 1.23.3

• add argument "emptyValue" to read.FCS API so that parser can still work correctly when either cases below occurs :
  1. there is double-delimiter in keyword values (sometime like \c:\path\...)
  2. there is empty keyword value (\keyword1\value1\keyword2\\keyword3)

flowCore 1.23.7

• fix the bug that malformed spillover matrix in write.FCS

flowCore 1.29.25

• Copied 'featureSignif' and other required functions from the 'feature' package into 'flowCore', to remove an undesired dependency on tcltk (caught in the dependency chain from 'feature'). These functions have been collated into 'feature.R'.

flowCore 1.31.15

• Deprecation
  • 'filterSet' and 'workFlow' are deprecated by 'flowWorkspace::GatingSet'
  • update vignette by using 'GatingSet'
• Enhancement
  • support 'SPILLOVERinread.FCS` besides the existing keywords ("SPILL", "spillover")
  • support reading(read.FCS ) bad FCS files exported by flowJo that do not follow standards strictly
  • support 'ncdfFlowList' in 'findTimeChannel' function

flowCore 1.37.6

• read.FCS
  • supports FCS that has diverse bit widths across parameters/channels
  • supports FCS that uses big integer (i.e. uint32 > R's integer.max) write.FCS
  • Fixes several bugs so that this API is now more usable

flowCore 1.47.10

• All documentation converted converted to roxygen2 with some additions and reorganization

flowCore 1.53.x

• 'workFlow' class and related classes and methods now defunct #148 -- superseded by flowWorkspace
• Add support for multiple data segments in 'read.FCSheader'
• Fixed some edge cases with 'read.FCS 'with column.pattern argument #157
• Added 'transform_gate' methods for geometric transformations of gates
• Added 'collapse_desc' for coercing keyword lists in to character
• 'spillover' method for calculating compensation matrix from a 'flowSet' of controls moved to 'flowStats'
• Added 'filter_keywords' for filtering lists of keywords
• Deprecate description and description<- for keyword and keyword<- to reduce redundancy and give consistent behavior for cytoframe RGLab/flowWorkspace #311

flowCore 2.0.0

• keyword<- behaves now as normal replacement method, i.e. keyword(fr) <- list(name = value) will replace the entire keyword list instead of partial updating/inserting, to achieve latter, use keyword(fr)["name"] <- value
• [ method (e.g. fr[, 1:4]) no longer deletes $PnX keywords automatically so that it is compatible with cytoframe

RGLab/flowCore documentation built on Aug. 26, 2024, 8:52 a.m.