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add version argument for writing gene expression to hdf5#2161

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szcf-weiya wants to merge 1 commit intoGreenleafLab:devfrom
szcf-weiya:dev-patch1
Open

add version argument for writing gene expression to hdf5#2161
szcf-weiya wants to merge 1 commit intoGreenleafLab:devfrom
szcf-weiya:dev-patch1

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@szcf-weiya
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I noticed that the current package has introduced version argument, along with other new arguments in the addMatToArrow function,

ArchR/R/ArrowWrite.R

Lines 105 to 126 in 65968a4

.addMatToArrow <- function(
mat = NULL,
ArrowFile = NULL,
Group = NULL,
binarize = FALSE,
addRowSums = FALSE,
addColSums = FALSE,
addRowMeans = FALSE,
addRowVars = FALSE,
addColMeansLog2 = FALSE, #New
addRowMeansLog2 = FALSE, #New
addRowVarsLog2 = FALSE,
addRowMeansGeo = FALSE, #New
addRowVarsGeo = FALSE, #New
addRowSumsBinary = FALSE, #New
addColSumsBinary = FALSE, #New
addRowMeansLog2Norm = FALSE, #New
addRowVarsLog2Norm = FALSE, #New
scaleTo = 10000, #New
colSm = NULL, #New
logFile = NULL,
version = 2 #New

but the higher-level function addGeneExpressionMatrix does not support passing those new arguments.

This pull request aims to provide the option to use the hdf5 style of the old version (version = 1).

@immanuelazn immanuelazn force-pushed the dev branch 3 times, most recently from 322676f to f6fcc50 Compare January 22, 2025 05:24
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