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BDS
GeneDER
ArrayUtils
Commits
7cb20fd2
Commit
7cb20fd2
authored
Jul 11, 2019
by
Leon-Charles Tranchevent
Browse files
Added GC-RMA support for Affymetrix arrays.
parent
fdeae68b
Changes
3
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DESCRIPTION
View file @
7cb20fd2
...
...
@@ -14,6 +14,7 @@ Imports:
utils,
stats,
affy,
gcrma,
arrayQualityMetrics,
SCAN.UPC,
massiR,
...
...
R/preprocess_data.R
View file @
7cb20fd2
...
...
@@ -47,14 +47,14 @@ preprocess_data <- function(input_data_dir, output_data_file,
batch_filename
=
batch_filename
,
clean_samples
=
clean_samples
,
verbose
=
verbose
)
}
else
if
(
method
==
"RMA"
)
{
eset
<-
preprocess_data_affymetrix_rma
(
input_data_dir
,
output_data_file
,
compressed
=
compressed
,
batch_correction
=
batch_correction
,
batch_filename
=
batch_filename
,
clean_samples
=
clean_samples
,
verbose
=
verbose
)
}
else
if
(
method
==
"
GC
RMA"
)
{
eset
<-
preprocess_data_affymetrix_
gc
rma
(
input_data_dir
,
output_data_file
,
compressed
=
compressed
,
batch_correction
=
batch_correction
,
batch_filename
=
batch_filename
,
clean_samples
=
clean_samples
,
verbose
=
verbose
)
}
}
else
if
(
platform
==
"Agilent"
)
{
eset
<-
preprocess_data_agilent_limma
(
input_data_dir
,
...
...
R/preprocess_data_affymetrix_rma.R
→
R/preprocess_data_affymetrix_
gc
rma.R
View file @
7cb20fd2
#' @title Preprocess an Affymetrix dataset with RMA.
#' @title Preprocess an Affymetrix dataset with
GC-
RMA.
#'
#' @description This function preprocess an Affymetrix dataset using RMA and saves the
#' results in a given TSV file. In addition, it returns the ESET object.
...
...
@@ -22,7 +22,7 @@
#' @param verbose A boolean representing whether the function should display log information. This
#' is TRUE by default.
#' @return The expression data as an ESET object.
preprocess_data_affymetrix_rma
<-
function
(
input_data_dir
,
output_data_file
,
preprocess_data_affymetrix_
gc
rma
<-
function
(
input_data_dir
,
output_data_file
,
compressed
=
FALSE
,
batch_correction
=
FALSE
,
batch_filename
=
"Batch.tsv"
,
...
...
@@ -36,7 +36,7 @@ preprocess_data_affymetrix_rma <- function(input_data_dir, output_data_file,
input_data_files
<-
affy
::
list.celfiles
(
raw_data_input_dir
,
full.names
=
TRUE
)
remove
(
raw_data_input_dir
)
batch
<-
affy
::
ReadAffy
(
filenames
=
input_data_files
,
compress
=
compressed
,
verbose
=
verbose
)
eset
<-
affy
::
rma
(
batch
)
eset
<-
gcrma
::
gc
rma
(
batch
)
# If necessary, we remove the samples that do not have clinical data.
if
(
clean_samples
)
{
...
...
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