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Improve diff tissue composition #139

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merged 10 commits into from
Jan 12, 2021
Merged

Improve diff tissue composition #139

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cc952ac
custom prefix for deconvolution
stemangiola Nov 13, 2020
34f6a17
add multivariable framework
stemangiola Nov 13, 2020
5c8431e
update manual
stemangiola Nov 13, 2020
29318c3
update framework and tests
stemangiola Nov 16, 2020
960e276
add immunedeconv
stemangiola Nov 16, 2020
384fcee
drop broom dependency
stemangiola Nov 16, 2020
07aa31e
make reference the default for each algorithm
stemangiola Nov 23, 2020
ab7835c
edit tests
stemangiola Jan 12, 2021
a936a29
avoid parallel for cibersort for cores=1
stemangiola Jan 12, 2021
67d70f0
update dependencies
stemangiola Jan 12, 2021
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3 changes: 2 additions & 1 deletion DESCRIPTION
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Expand Up @@ -64,7 +64,8 @@ Suggests:
pasilla,
ggrepel,
devtools,
functional
functional,
immunedeconv
VignetteBuilder:
knitr
RdMacros:
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4 changes: 4 additions & 0 deletions NAMESPACE
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Expand Up @@ -110,6 +110,7 @@ importFrom(purrr,map)
importFrom(purrr,map2)
importFrom(purrr,map2_dfr)
importFrom(purrr,map_dfr)
importFrom(purrr,map_lgl)
importFrom(purrr,reduce)
importFrom(purrr,when)
importFrom(rlang,":=")
Expand Down Expand Up @@ -143,7 +144,10 @@ importFrom(stats,rnorm)
importFrom(stats,sd)
importFrom(stats,setNames)
importFrom(stats,terms)
importFrom(stringr,str_remove)
importFrom(stringr,str_replace)
importFrom(stringr,str_replace_all)
importFrom(stringr,str_split)
importFrom(tibble,as_tibble)
importFrom(tibble,tibble)
importFrom(tidyr,complete)
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5 changes: 3 additions & 2 deletions R/cibersort.R
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Expand Up @@ -64,8 +64,9 @@ CoreAlg <- function(X, y, cores = 3){
}

#Execute In a parallel way the SVM
if(Sys.info()['sysname'] == 'Windows') out <- mclapply(1:svn_itor, res, mc.cores=1) else
out <- mclapply(1:svn_itor, res, mc.cores=cores) #lapply(1:svn_itor, res) #
if(Sys.info()['sysname'] == 'Windows') out <- mclapply(1:svn_itor, res, mc.cores=1)
else if(cores>1) out <- mclapply(1:svn_itor, res, mc.cores=cores)
else out <- lapply(1:svn_itor, res)

#Initiate two variables with 0
nusvm <- rep(0,svn_itor)
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