View source: R/summarizeExperiment.R
summarizeExperiment | R Documentation |
Combine multiple sequence lists (as returned by digestFastqs
into a SummarizedExperiment
, with
observed variable sequences (sequence pairs) in rows and samples in columns.
summarizeExperiment(x, coldata, countType = "umis")
x |
A named list of objects returned by |
coldata |
A |
countType |
Either "reads" or "umis". If "reads", the "count" assay of the returned object will contain the observed number of reads for each sequence (pair). If "umis", the "count" assay will contain the number of unique UMIs observed for each sequence (pair). |
A SummarizedExperiment
x
with
containing the observed number of sequences or
sequence pairs (if countType
= "reads"), or the observed number of
unique UMIs for each sequence or sequence pair (if countType
=
"umis").
containing the unique sequences or sequence pairs.
containing the metadata provided by coldata
.
Michael Stadler, Charlotte Soneson
## Input sample
inp <- digestFastqs(
fastqForward = system.file("extdata", "cisInput_1.fastq.gz",
package = "mutscan"),
elementsForward = "SUCV", elementLengthsForward = c(1, 10, 18, 96),
constantForward = "AACCGGAGGAGGGAGCTG",
wildTypeForward = c(FOS = paste0("ACTGATACACTCCAAGCGGAGACAGACCAACTAGAAGATGAGAAGTC",
"TGCTTTGCAGACCGAGATTGCCAACCTGCTGAAGGAGAAGGAAAAACTA")),
nbrMutatedCodonsMaxForward = 1
)
## Output sample
outp <- digestFastqs(
fastqForward = system.file("extdata", "cisOutput_1.fastq.gz",
package = "mutscan"),
elementsForward = "SUCV", elementLengthsForward = c(1, 10, 18, 96),
constantForward = "AACCGGAGGAGGGAGCTG",
wildTypeForward = c(FOS = paste0("ACTGATACACTCCAAGCGGAGACAGACCAACTAGAAGATGAGAAGTC",
"TGCTTTGCAGACCGAGATTGCCAACCTGCTGAAGGAGAAGGAAAAACTA")),
nbrMutatedCodonsMaxForward = 1
)
## Combine
se <- summarizeExperiment(
x = list(r1inp = inp, r1outp = outp),
coldata = data.frame(Name = c("r1inp", "r1outp"),
Condition = c("input", "output"),
Replicate = c("rep1", "rep1")),
countType = "umis"
)
se
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