Description Usage Arguments Details Value Examples
View source: R/deeptools_funs.R
Loads a deeptools v3 matrix file.
1 2 3 4 5 6 7 |
fname |
the file to load. |
na.fill |
Fills NAs with this value zero. Default is 0. |
as.matrix |
Return matrix as matrix (default is FALSE, ie returns tidy data.frame instead) |
as.S3 |
Return S3 class metagene object, see details for more info |
Loads a gzipped deeptools matrix file and collects this in a
tidy
data.frame. If as.matrix is true, the header information is
added as attribute.
as.S3 returns a metagene object, with slots: $header, $regions, $samples,
$groups and $matrices. Where $header contains the header information as a
named vector. Matrices is a list of matrices where each matrix is specific
to 1 sample and 1 group. $samples are the samplenames for each matrix.
$groups are the groups for each matrix.
An object of class deeptools_matrix
with provided means and covariances
computed as 1/alpha
.
1 2 3 4 5 6 7 8 9 10 11 | fname <- system.file("extdata", "deeptools3_matrix.gz", package = "RMetaTools")
df <- load_deeptoolsmatrix3(fname)
head(df)
df_withNAas0 <- load_deeptoolsmatrix3(fname, na.fill=0)
head(df_withNAas0)
s3obj <- load_deeptoolsmatrix3(fname, na.fill=0, as.S3=TRUE)
head(s3obj$regions)
lapply(s3obj$matrices, head)
s3obj$samples
s3obj$groups
lapply(s3obj$rel_pos, head)
|
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