Extrating out the getMarkerFeatures

[mano2991]

I have two samples in my ArchR file. I need to compare them. So I used the getMarkerFeatures to do a pairwise comparison in my data. This gives me Log2Fold change, FDR, Pvalue, Mean, AUC, etc I can plot a heatmap, and Volcanotplot using these values while extracting the data. using getPeaks for the peak file and getMarkers for the genescore matrix I'm not able to extract the information it always gives me the FDR value along with the Gene Name for the genescore Matrix file and Peaks it gives me the peak locating along with FDR and Log2Fold change hence I made a custom script.

Is there any other way to extract the information instead of manually?

markersPeaks <- getMarkerFeatures(
    ArchRProj = proj5, 
    useMatrix = "PeakMatrix", 
    groupBy = "Sample",
  bias = c("TSSEnrichment", "log10(nFrags)"),
  testMethod = "wilcoxon",
  useGroups = "Uninjured",
  bgdGroups = "Injured_7dpi"
)

A custom script for extracting the Peak file

# Load necessary library
library(SummarizedExperiment)

# Extract necessary data from elementMetadata
element_metadata <- elementMetadata(markersPeaks)
seqnames <- as.character(element_metadata$seqnames)
start <- element_metadata$start
end <- element_metadata$end

# Extract assay data
log2FC <- markersPeaks@assays@data@listData$Log2FC$x
mean <- markersPeaks@assays@data@listData$Mean$x
fdr <- markersPeaks@assays@data@listData$FDR$x
pval <- markersPeaks@assays@data@listData$Pval$x
meanDiff <- markersPeaks@assays@data@listData$MeanDiff$x
auc <- markersPeaks@assays@data@listData$AUC$x
meanBGD <- markersPeaks@assays@data@listData$MeanBGD$x

# Check the length of extracted data to ensure they are consistent
lengths <- sapply(list(seqnames, start, end, log2FC, mean, fdr, pval, meanDiff, auc, meanBGD), length)
names(lengths) <- c("seqnames", "start", "end", "log2FC", "mean", "fdr", "pval", "meanDiff", "auc", "meanBGD")
print(lengths)

# Combine extracted values into a data frame
if (all(lengths == lengths[1])) {
  peak_data <- data.frame(
    seqnames = seqnames,
    start = start,
    end = end,
    Log2FC = log2FC,
    Mean = mean,
    FDR = fdr,
    Pval = pval,
    MeanDiff = meanDiff,
    AUC = auc,
    MeanBGD = meanBGD
  )

  # Write the data frame to a CSV file
  write.csv(peak_data, "markersPeaks.csv", row.names = FALSE)
} else {
  stop("The lengths of the extracted data do not match.")
}

A custom script for the extracting the gene information.

# Extract seqnames with the correct length
seqnames <- rep(as.character(markersPeaks_GS@elementMetadata@listData$seqnames@values), markersPeaks_GS@elementMetadata@listData$seqnames@lengths)

# Combine genomic information
genomic_info <- data.frame(
  seqnames = seqnames,
  start = markersPeaks_GS@elementMetadata@listData$start,
  end = markersPeaks_GS@elementMetadata@listData$end,
  name = markersPeaks_GS@elementMetadata@listData$name
)

# Extract assay data
log2fc <- markersPeaks_GS@assays@data@listData$Log2FC$x
mean <- markersPeaks_GS@assays@data@listData$Mean$x
fdr <- markersPeaks_GS@assays@data@listData$FDR$x
pval <- markersPeaks_GS@assays@data@listData$Pval$x
mean_diff <- markersPeaks_GS@assays@data@listData$MeanDiff$x
auc <- markersPeaks_GS@assays@data@listData$AUC$x
mean_bgd <- markersPeaks_GS@assays@data@listData$MeanBGD$x

# Combine all data into a single data frame
combined_data <- data.frame(
  genomic_info,
  Log2FC = log2fc,
  Mean = mean,
  FDR = fdr,
  Pval = pval,
  MeanDiff = mean_diff,
  AUC = auc,
  MeanBGD = mean_bgd
)

# Write the combined data frame to a CSV file
write.csv(combined_data, file = "Gene_score_Pairwise_patz1_7dpi.csv", row.names = FALSE)

[rcorces]

Hi @mano2991! Thanks for using ArchR! Lately, it has been very challenging for me to keep up with maintenance of this package and all of my other
responsibilities as a PI. I have not been responding to issue posts and I have not been pushing updates to the software. We are actively searching to hire
a computational biologist to continue to develop and maintain ArchR and related tools. If you know someone who might be a good fit, please let us know!
In the meantime, your issue will likely go without a reply. Most issues with ArchR right not relate to compatibility. Try reverting to R 4.1 and Bioconductor 3.15.
Newer versions of Seurat and Matrix also are causing issues. Sorry for not being able to provide active support for this package at this time.