Description Usage Arguments Value Author(s) References Examples
WARNING: readKallisto()
is deprecated. Please use tximeta()
from the tximeta package instead.
readKallisto
inputs several kallisto output files into a single
SummarizedExperiment
instance, with rows corresponding to
estimated transcript abundance and columns to
samples. readKallistoBootstrap
inputs kallisto bootstrap
replicates of a single sample into a matrix of transcript x bootstrap
abundance estimates.
1 2 3 4 5 6 | readKallisto(files,
json = file.path(dirname(files), "run_info.json"),
h5 = any(grepl("\\.h5$", files)), what = KALLISTO_ASSAYS,
as = c("SummarizedExperiment", "list", "matrix"))
readKallistoBootstrap(file, i, j)
|
files |
character() paths to kallisto ‘abundance.tsv’ output files. The assumption is that files are organized in the way implied by kallisto, with each sample in a distinct directory, and the directory containing files abundance.tsv, run_info.json, and perhaps abundance.h5. |
json |
character() vector of the same length as |
h5 |
character() vector of the same length as |
what |
character() vector of kallisto per-sample outputs to be input. See KALLISTO_ASSAYS for available values. |
as |
character(1) specifying the output format. See |
file |
character(1) path to a single HDF5 output file. |
i, j |
integer() vector of row ( |
A SummarizedExperiment
, list
, or matrix
,
depending on the value of argument as
; by default a
SummarizedExperiment
. The as="SummarizedExperiment"
rowData(se)
the length of each transcript;
colData(se)
includes summary information on each sample,
including the number of targets and bootstraps, the kallisto and index
version, the start time and operating system call used to create the
file. assays()
contains one or more transcript x sample
matrices of parameters estimated by kallisto (see
KALLISTO_ASSAYS
).
as="list"
return value contains information simillar to
SummarizedExperiment
with row, column and assay data as
elements of the list without coordination of row and column
annotations into an integrated data container. as="matrix"
returns the specified assay as a simple R matrix.
Martin Morgan martin.morgan@roswellpark.org
http://pachterlab.github.io/kallisto software for quantifying transcript abundance.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 | ## Not run:
outputs <- system.file(package="SummarizedExperiment", "extdata",
"kallisto")
files <- dir(outputs, pattern="abundance.tsv", full=TRUE, recursive=TRUE)
stopifnot(all(file.exists(files)))
## default: input 'est_counts'
(se <- readKallisto(files, as="SummarizedExperiment"))
str(readKallisto(files, as="list"))
str(readKallisto(files, as="matrix"))
## available assays
KALLISTO_ASSAYS
## one or more assay
readKallisto(files, what=c("tpm", "eff_length"))
## alternatively: read hdf5 files
files <- sub(".tsv", ".h5", files, fixed=TRUE)
readKallisto(files)
## input all bootstraps
xx <- readKallistoBootstrap(files[1])
ridx <- head(which(rowSums(xx) != 0), 3)
cidx <- c(1:5, 96:100)
xx[ridx, cidx]
## selective input of rows (transcripts) and/or bootstraps
readKallistoBootstrap(files[1], i=c(ridx, rev(ridx)), j=cidx)
## End(Not run)
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.