A web version of gprofiler is available here: https://biit.cs.ut.ee/gprofiler/gost A vignette is here: https://cran.r-project.org/web/packages/gprofiler2/vignettes/gprofiler2.html#gene-identifier-conversion-with-gconvert
## Warning: replacing previous import 'variancePartition::hatvalues' by
## 'stats::hatvalues' when loading 'mvIC'i <- "LBDvsControl"
filepath <- paste0(
"../../../results/",
tool,
"/DEGs/",
condition,
"_",
i,
"_gene_DEGs_FDRq0.05_logFC_0.25.txt"
)
df <- assign(paste0(i),
tryCatch(
read.delim(
filepath,
header = TRUE,
sep = "\t",
stringsAsFactors = FALSE
),
error = function(e)
NULL
))
up <- subset(df$gene_name, df$logFC > 0, sort = FALSE)
assign(paste0(i, "_up"), up)
down <- subset(df$gene_name, df$logFC < 0, sort = FALSE)
assign(paste0(i, "_down"), down)
# gprofiler
gp_up <- gost(up, ordered_query = TRUE, organism = "hsapiens")
gp_down <- gost(down, ordered_query = TRUE, organism = "hsapiens")
#--- up LBD vs Control
# interactive plot
gostplot(gp_up, interactive = TRUE)#--- down LBD vs Control
# interactive plot
gostplot(gp_down, interactive = TRUE)## Warning in remove(combind, df, gp_down, gp_up, LBDvsControl, p_down, p_up, :
## object 'combind' not found## Warning in remove(combind, df, gp_down, gp_up, LBDvsControl, p_down, p_up, :
## object 'p_down' not found## Warning in remove(combind, df, gp_down, gp_up, LBDvsControl, p_down, p_up, :
## object 'p_up' not found## Warning in remove(combind, df, gp_down, gp_up, LBDvsControl, p_down, p_up, :
## object 'plot_down' not found## Warning in remove(combind, df, gp_down, gp_up, LBDvsControl, p_down, p_up, :
## object 'plot_up' not foundi <- "ADvsControl"
filepath <- paste0(
"../../../results/",
tool,
"/DEGs/",
condition,
"_",
i,
"_gene_DEGs_FDRq0.05_logFC_0.25.txt"
)
df <- assign(paste0(i),
tryCatch(
read.delim(
filepath,
header = TRUE,
sep = "\t",
stringsAsFactors = FALSE
),
error = function(e)
NULL
))
up <- subset(df$gene_name, df$logFC > 0, sort = FALSE)
assign(paste0(i, "_up"), up)
down <- subset(df$gene_name, df$logFC < 0, sort = FALSE)
assign(paste0(i, "_down"), down)
# gprofiler
gp_up <- gost(up, ordered_query = TRUE, organism = "hsapiens")
gp_down <- gost(down, ordered_query = TRUE, organism = "hsapiens")
#--- up AD vs Control
# interactive plot
gostplot(gp_up, interactive = TRUE)#--- down AD vs Control
# interactive plot
gostplot(gp_down, interactive = TRUE)## Warning in remove(combind, df, gp_down, gp_up, ADvsControl, p_down, p_up, :
## object 'combind' not found## Warning in remove(combind, df, gp_down, gp_up, ADvsControl, p_down, p_up, :
## object 'p_down' not found## Warning in remove(combind, df, gp_down, gp_up, ADvsControl, p_down, p_up, :
## object 'p_up' not found## Warning in remove(combind, df, gp_down, gp_up, ADvsControl, p_down, p_up, :
## object 'plot_down' not found## Warning in remove(combind, df, gp_down, gp_up, ADvsControl, p_down, p_up, :
## object 'plot_up' not foundi <- "LBDvsAD"
filepath <- paste0(
"../../../results/",
tool,
"/DEGs/",
condition,
"_",
i,
"_gene_DEGs_FDRq0.05_logFC_0.25.txt"
)
df <- assign(paste0(i),
tryCatch(
read.delim(
filepath,
header = TRUE,
sep = "\t",
stringsAsFactors = FALSE
),
error = function(e)
NULL
))
up <- subset(df$gene_name, df$logFC > 0, sort = FALSE)
assign(paste0(i, "_up"), up)
down <- subset(df$gene_name, df$logFC < 0, sort = FALSE)
assign(paste0(i, "_down"), down)
# gprofiler
gp_up <- gost(up, ordered_query = TRUE, organism = "hsapiens")
gp_down <- gost(down, ordered_query = TRUE, organism = "hsapiens")
#--- up LBD vs AD
# interactive plot
gostplot(gp_up, interactive = TRUE)#--- down LBD vs AD
# interactive plot
gostplot(gp_down, interactive = TRUE)