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BDS
GeneDER
ArrayUtils
Commits
231e050f
Commit
231e050f
authored
Jun 18, 2019
by
Leon-Charles Tranchevent
Browse files
Replaced probe ids by probe names for Agilent data processing.
parent
ccb29793
Changes
2
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Inline
Side-by-side
R/preprocess_data_agilent_limma.R
View file @
231e050f
...
...
@@ -40,6 +40,9 @@ preprocess_data_agilent_limma <- function(input_data_dir, output_data_file,
green.only
=
TRUE
,
verbose
=
TRUE
)
batch_data
<-
log2
(
batch
$
E
)
# We change the probe ids (1 to 45015) to be the probe names instead (A_XX_PXXXX).
rownames
(
batch_data
)
<-
(
batch
$
genes
)
$
ProbeName
remove
(
raw_data_input_dir
,
batch
)
# We run the LIMMA pre-processing method on the data.
...
...
@@ -61,6 +64,11 @@ preprocess_data_agilent_limma <- function(input_data_dir, output_data_file,
batch_data_norm
<-
batch_data_norm
[,
samples
]
}
# We remove the duplicate rows (based on the row names only).
probe_id_counts
<-
table
(
row.names
(
batch_data
))
unique_probe_ids
<-
setdiff
(
names
(
probe_id_counts
),
names
(
probe_id_counts
[
probe_id_counts
>
1
]))
batch_data_norm
<-
batch_data_norm
[
unique_probe_ids
,
]
# We save the eset data as TSV file.
eset
<-
methods
::
new
(
"ExpressionSet"
,
exprs
=
as.matrix
(
batch_data_norm
))
rm
(
batch_data_bg
)
...
...
R/read_eset.R
View file @
231e050f
...
...
@@ -7,18 +7,21 @@
#' @param data_file A string representing the file that contains the expression data.
#' @param header A boolean indicating whether the file contains a header (default to TRUE).
#' @param sep A string that is used as a field separator to read the data (default to
#'
tab for TSV files).
#' tab for TSV files).
#' @param row_names The index of the row names (default to 1).
#' @param as_is A boolean indicating whether R should keep the data as they are in the
#' file (default to TRUE).
#' file (default to TRUE).
#' @param as_eset A boolean indicating whether the returned object should be an eset. A matrix
#' is returned otherwise. Default to TRUE.
#' @param verbose A boolean representing whether the function should display log information. This
#'
is TRUE by default.
#' @return An
ExpressionSe
t containing the
preprocessed
expression data.
#' is TRUE by default.
#' @return An
objec
t containing the expression data
. Either an ExpressionSet or a Matrix
.
read_eset
<-
function
(
data_file
,
header
=
TRUE
,
sep
=
"\t"
,
row_names
=
1
,
as_is
=
TRUE
,
as_eset
=
TRUE
,
verbose
=
TRUE
)
{
# We load the matrix and creates the associated eset object.
...
...
@@ -30,11 +33,14 @@ read_eset <- function(data_file,
exprs_eset
<-
Biobase
::
ExpressionSet
(
assayData
=
exprs_mat
)
# We clean up and log information.
rm
(
exprs_mat
)
if
(
verbose
==
TRUE
)
{
message
(
paste0
(
"["
,
Sys.time
(),
"] Expression data read."
))
}
# We return the eset.
return
(
exprs_eset
)
# We return the object.
if
(
as_eset
)
{
return
(
exprs_eset
)
}
else
{
return
(
exprs_mat
)
}
}
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