Easy label transfer from reference data

This function retrieves data from malaria.tools and generates a dataframe containing the Stage of Parasite in which the gene is highly expressed.

Usage

easyLabelTransfer(
  queryCounts,
  refCounts,
  referenceMeta,
  refNormalised = FALSE,
  queryNormalised = FALSE,
  labelCol,
  isrefBulk = FALSE,
  ...
)

Arguments

queryCounts

A object containing the raw counts or lognormalised counts of query dataset. It can be in form of dcgMatrix. If the counts are normalised, set queryNormalised=TRUE.

refCounts

description A object containing the raw counts or lognormalised counts of reference dataset. It can be in form of dcgMatrix. If the counts are normalised, set refNormalised=TRUE.

referenceMeta

A dataframe containing the reference metadata.

refNormalised

Logical. Use TRUE, if the counts are already normalised otherwise counts are log-normalised using Scuttle's logNormCounts function.

queryNormalised

Logical. Use TRUE, if the counts are already normalised otherwise counts are log-normalised using Scuttle's logNormCounts function.

labelCol

Column of the metadata that contains the desired labels to be transferred to the query.

isrefBulk

Logical. Use TRUE, if the reference dataset is Bulk-RNASeq. In such cases "classic" approach is used to shortlist DEGs. If false, "wilcox" method will be used for scRNAseq reference.

...

Additional arguments that can be passed to SingleR based on user's needs such as de.n=30 or aggr.ref=TRUE. Refer to SingleR documentation for further details.

Value

A DFrame object containing transferred labels which can be directly used with other functions of SingleR such as plotScoreHeatmap().

Examples

if (FALSE) { # \dontrun{
## Fetching the URL
mcalist <- listMCA()
data("subudhi2020") ## reference dataset

## Using this reference set
url <- "https://www.malariacellatlas.org/downloads/pf-ch10x-set4-biorxiv.zip"

raw_counts <- easyMCA(url,type = "raw")
rownames(raw_counts) <- gsub("-","_",rownames(raw_counts))
meta <- easyMCA(url,type="data")

## Retaining only Asexual stage cells and Lab isolates.
meta <- subset(meta, meta$STAGE_LR %in% c("ring","trophozoite","schizont") & DAY != "Field")
raw_counts <- raw_counts[,rownames(meta)]

## Filtering away field isolates and asexual stage cells
labels <- easyLabelTransfer(queryCounts = raw_counts,
refCounts = subudhi2020@assays@data$counts,
referenceMeta = subudhi2020@colData,
labelCol = "timetag", isrefBulk = TRUE)
} # }