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New Release v1.4.0 #120

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merged 12 commits into from
Mar 9, 2021
Merged

New Release v1.4.0 #120

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3805704
Update ATACRunSeurat with Signac functions, and update Incorporate wi…
DongqingSun Feb 23, 2021
3968083
Update DESCRIPTION and NAMESPACE for changes in ATAC functions
DongqingSun Feb 23, 2021
bdefd82
Update packages in conda meta file
DongqingSun Feb 23, 2021
ef0cdc2
Merge pull request #9 from DongqingSun96/fix/Seurat4
baigal628 Feb 28, 2021
078b737
updated lisa ref
baigal628 Feb 28, 2021
155627d
Update Package version
baigal628 Mar 1, 2021
f772101
add outdir path to the MAESTRO R functions
baigal628 Mar 5, 2021
7b73166
add outdir variables to MAESTRO R
baigal628 Mar 5, 2021
7ce27ed
update docs as 1.4.0
baigal628 Mar 5, 2021
2481dc0
update docs as 1.4.0
baigal628 Mar 5, 2021
8ffc85d
update docs as 1.4.0
baigal628 Mar 5, 2021
f561ee1
fix bugs in path change
baigal628 Mar 6, 2021
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fix bugs in path change
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@baigal628
baigal628 committed Mar 6, 2021
commit f561ee15230b94a5261d4c8c9c5957f764264d8d
16 changes: 8 additions & 8 deletions R/RNAAnnotateTranscriptionFactor.R
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Original file line number Diff line number Diff line change
Expand Up @@ -67,16 +67,16 @@ RNAAnnotateTranscriptionFactor <- function(RNA, genes, cluster = NULL, project =
method = toupper(method)
if(method == "RABIT"){
scorename = "log(Rabitscore)"
out_fdr_max_log = tryCatch(expr = RunRABIT(genes = genes, project = project, rabit.path = rabit.path, organism = org),
out_fdr_max_log = tryCatch(expr = RunRABIT(genes = genes, project = project, rabit.path = rabit.path, organism = org, outdir="."),
error = function(cond) {return(cond$message)})
}
if(method == "LISA"){
scorename = "log(Lisascore)"
if(lisa.mode == "multi"){
out_fdr_max_log = RunLISAMulti(genes = genes, project = project, organism = organism, lisa.path = lisa.path)
out_fdr_max_log = RunLISAMulti(genes = genes, project = project, organism = organism, lisa.path = lisa.path, outdir=".")
}
if(lisa.mode == "one-vs-rest"){
out_fdr_max_log = RunLISAWeb(genes = genes, project = project, organism = organism)
out_fdr_max_log = RunLISAWeb(genes = genes, project = project, organism = organism, outdir=".")
}
}

Expand Down Expand Up @@ -210,7 +210,7 @@ RNAAnnotateTranscriptionFactor <- function(RNA, genes, cluster = NULL, project =
}


RunLISAMulti <- function(genes, project, organism = "GRCh38", lisa.path = lisa.path)
RunLISAMulti <- function(genes, project, organism = "GRCh38", lisa.path = lisa.path, outdir=".")
{
if(organism == "GRCh38"){
species = "hg38"
Expand Down Expand Up @@ -267,7 +267,7 @@ RunLISAMulti <- function(genes, project, organism = "GRCh38", lisa.path = lisa.p
return(tf_all_log10)
}

RunLISAWeb <- function(genes, project, organism = "GRCh38")
RunLISAWeb <- function(genes, project, organism = "GRCh38", outdir=".")
{
if(organism == "GRCh38"){
species = "hg38"
Expand All @@ -278,7 +278,7 @@ RunLISAWeb <- function(genes, project, organism = "GRCh38")

cluster_markers_list <- split(genes, genes$cluster)

outputDir <- paste0(project, ".lisa")
outputDir <- file.path(outdir, paste0(project, ".lisa"))
if (!file.exists(outputDir)) dir.create(path=outputDir)

res_zip_url_list = rep("zip", length(cluster_markers_list))
Expand Down Expand Up @@ -382,7 +382,7 @@ DownloadResult <- function(resurl, destfile)
}


RunRABIT <- function(genes, project, rabit.path, organism = "hsa")
RunRABIT <- function(genes, project, rabit.path, organism = "hsa", outdir=".")
{
if(organism == "hsa"){
genes$entrezid = MAGeCKFlute::TransGeneID(genes$gene, fromType = "Symbol", toType = "Entrez",
Expand All @@ -401,7 +401,7 @@ RunRABIT <- function(genes, project, rabit.path, organism = "hsa")
genes = na.omit(genes)
cluster_markers_list <- split(genes, genes$cluster)

outputDir <- paste0(project, ".RABIT")
outputDir <- file.path(outdir, paste0(project, ".RABIT"))
if (!file.exists(outputDir)){
dir.create(path=outputDir)
}else{
Expand Down