predict_age_fromse {RNAAgeCalc} | R Documentation |
Calculate RNA age using SummarizedExperiment
Description
This function takes SummarizedExperiment object as input and
calculates RNA age.
Usage
predict_age_fromse(
se,
tissue,
exprtype = c("FPKM", "counts"),
idtype = c("SYMBOL", "ENSEMBL", "ENTREZID", "REFSEQ"),
stype = c("all", "caucasian"),
signature = NULL,
maxp = NULL
)
Arguments
se |
a SummarizedExperiment object. The assays(se) should
contain gene expression data. The name of assays(se) should be either "FPKM"
or "counts". Use 'exprtype' argument to specify the type of gene expression
data provided. Users are able to provide the chronological age of samples
using colData(se). This is optional. If provided, the column name for
chronological age in colData(se) should be "age". If some samples'
chronological age are not available, users are expected to set the
chronological age in colData(se) to NA. If chronological age is not
provided, the age acceleration residual will not be calculated. See package
vignette for the definition of age acceleration residual. In addition, users
are able to provide their own gene length using rowData(se). This is also
optional. If using 'exprtype = "FPKM"', the provided gene length will be
ignored. If provided, the column name for gene length in rowData(se) should
be "bp_length". The function will convert raw count to FPKM by the
user-supplied gene length. Otherwise, gene length is obtained from the
internal database. See below for an example of se object.
|
tissue |
a string indicate which tissue the gene expression data is
obtained from. Users are expected to provide one of the following tissues.
If the tissue argument is not provide or the provided tissue is not in this
list, then the age predictor trained on all tissues will be used to
calculate RNA age.
adipose_tissue
adrenal_gland
blood
blood_vessel
brain
breast
colon
esophagus
heart
liver
lung
muscle
nerve
ovary
pancreas
pituitary
prostate
salivary_gland
skin
small_intestine
spleen
stomach
testis
thyroid
uterus
vagina
|
exprtype |
either "counts" or "FPKM". For RPKM data, please use
'exprtype' = "FPKM".
|
idtype |
a string which indicates the gene id type in 'exprdata'.
It should be one of "SYMBOL", "ENSEMBL", "ENTREZID" or "REFSEQ". Default is
"SYMBOL".
|
stype |
a string which specifies which version of pre-trained
calculators to be used. It should be either "all" or "Caucasian". "all"
means samples from all races (American Indian/Alaska Native, Asian,
Black/African American, and Caucasian) are used to obtain the
pre-trained calculator. "Caucasian" means only the Caucasian samples are
used to build up the pre-trained calculator.
|
signature |
a string which indicates the age signature to use when
calculating RNA age. This argument is not required.
In the case that this argument is not provided, if 'tissue' argument is also
provided and the tissue is in the list above, the tissue specific age
signature given by our DESeq2 analysis result on GTEx data will be used.
Otherwise, the across tissue signature "GTExAge" will be used.
In the case that this argument is provided, it should be one of the
following signatures. A detailed description of the meaning of these
signatures is given in the package vignette.
DESeq2
Pearson
Dev
deMagalhaes
GenAge
GTExAge
Peters
all
|
maxp |
the maxp argument used in impute.knn
function. This is optional.
|
Value
a data frame contains RNA age.
Examples
library(SummarizedExperiment)
data(fpkmExample)
colData = data.frame(age = c(40, 50))
se = SummarizedExperiment(assays=list(FPKM=fpkm),
colData=colData)
res = predict_age_fromse(se = se, exprtype = "FPKM")
[Package
RNAAgeCalc version 1.0.2
Index]