RunDEXSeq

Source code

Description

This will test the test features and binding features are different expressed between groups with a generalised linear model. See DEXSeq (PMID: 22722343) paper for details.

Usage

RunDEXSeq(
  object = NULL,
  bind.name = "gene_name",
  ident.1 = NULL,
  ident.2 = NULL,
  cells.1 = NULL,
  cells.2 = NULL,
  assay = NULL,
  bind.assay = NULL,
  features = NULL,
  bind.features = NULL,
  min.pct = 0.05,
  min.pct.bind.feature = 0.05,
  return.thresh = NULL,
  node = NULL,
  pseudo.group = 3,
  mode = 1,
  threads = 1,
  debug = FALSE
)

Arguments

object A Seurat object.
bind.name The title of binding name in meta table. Usually be “gene_name” for alternative splicing.
ident.1 Identify class to test, if not set will compare all groups one by one
ident.2 A second class for comparsion. If NULL (default), use all other cells for comparison.
cells.1 Vector of cell names belong to group 1. Conflict with ident.1
cells.2 Vector of cell names for comparsion. Conflict with ident.2
assay Assay for test features. Default assay will be used if not set.
bind.assay Assay for binding features. If not set, test features in same goup (with same bind name) will be aggreated as binding feature
features Candidate list to test. If not set, will use all.
bind.features Candidate list for binding features. If not set, will use all.
min.pct Only test features that are detected in a minimum fraction of min.pct cells in all cells. Meant to speed up the function by not testing genes that are very infrequenctly expressed in all cells. Remember we are testing alternative epxression pattern here, so it is possible the test feature is not expressed in one group, therefore we are not going to check by groups. Note that min.pct is set for test feature here. But in RunPSI, the min.pct is set for binding feature. Default is 0.05.
min.pct.bind.feature Only test binding features that are detected in a minimum fraction of min.pct.bind.feature in either of the two populations. Meant to speed up the function by not testing genes that are very infrequenctly expressed in both groups. Default is 0.05.
return.thresh Only return markers that have a p-value < return.thresh.
node A node to find markers for and all its children; requires BuildClusterTree to have been run previously. Only can be used if test all groups.
pseudo.group Aggregate single cells into pseudo groups, because DEXSeq is designed for bulk RNA-seq. At least 3 cells are required for each group. Default is 3.
mode Test mode, default is 1. See online manual for the difference between modes. <https://shiquan.github.io/Yano.html>
threads Threads passed to DEXSeq. Default is 1.

Value

Data frame containing p values and pct for test features and their binding features.

Examples

library("Yano")

data("glbt_small")
DefaultAssay(glbt_small) <- "exon"
glbt_small <- ParseExonName(glbt_small)
alt.exon <- RunDEXSeq(object = glbt_small, assay = "exon", bind.assay = "RNA", bind.name = "gene_name",ident.1 = "0", features = rownames(glbt_small))
head(alt.exon)
                                                            feature       pct.1
chr1:154169305-154169383/-/TPM3     chr1:154169305-154169383/-/TPM3 0.004102564
chr11:35197162-35197793/+/CD44       chr11:35197162-35197793/+/CD44 0.422564103
chr11:75421727-75422280/+/RPS3       chr11:75421727-75422280/+/RPS3 0.164102564
chr11:123060825-123061329/-/HSPA8 chr11:123060825-123061329/-/HSPA8 0.087179487
chr11:123061588-123061833/-/HSPA8 chr11:123061588-123061833/-/HSPA8 0.065641026
chr11:123061869-123062022/-/HSPA8 chr11:123061869-123062022/-/HSPA8 0.019487179
                                       pct.2 bind.feature      log2fc
chr1:154169305-154169383/-/TPM3   0.05073171         TPM3          NA
chr11:35197162-35197793/+/CD44    0.32097561         CD44          NA
chr11:75421727-75422280/+/RPS3    0.05268293         RPS3          NA
chr11:123060825-123061329/-/HSPA8 0.13951220        HSPA8  0.05078704
chr11:123061588-123061833/-/HSPA8 0.08780488        HSPA8 -0.44071765
chr11:123061869-123062022/-/HSPA8 0.04195122        HSPA8  0.31086581
                                           pval          padj
chr1:154169305-154169383/-/TPM3    7.392274e-11  2.841919e-09
chr11:35197162-35197793/+/CD44    3.763464e-116 1.302159e-113
chr11:75421727-75422280/+/RPS3     1.315600e-17  6.502825e-16
chr11:123060825-123061329/-/HSPA8  1.955408e-08  6.547463e-07
chr11:123061588-123061833/-/HSPA8  1.135199e-01  6.810299e-01
chr11:123061869-123062022/-/HSPA8  2.089351e-02  2.285663e-01
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