pd: A list of phenotype data.frames

In LieberInstitute/brainflowprobes: Plots and annotation for choosing BrainFlow target probe sequence

A list of phenotype data.frames

Description

A list of four phenotype data frames used throughput the package.

Format

A list of four data.frames:

Sep

phenotype information for samples from https://www.biorxiv.org/content/10.1101/567966v1; a data.frame with 23 rows and 15 columns. Column descriptions: SampleID is the sample name, Zone is the RNA fraction of the sample ("Nucleus" or "Cytosol"), Age, Sex, and Race list these demographic characteristics, Fetal categorizes each sample age as "Fetal" or "Adult", Library categorizes the RNAseq library preparation method as polyA selection ("polyA") or rRNA depletion ("RiboZero"), RIN_fraction is the RNA Integrity Number for each sample, sumMapped is the number of mapped reads, Shortlabels, Label, col, and LabelFrac are columns of information for plotting, BigWig is the name of the BigWig file for each sample, and files lists the URL for the BigWig online.

Deg

phenotype information for samples from https://www.pnas.org/content/114/27/7130; a data.frame with 40 rows and 16 columns. Column descriptions: DegradationTime is the number of minutes the brain tissue for each sample was left on the benchtop at room temperature before RNA was extracted, AgeDeath is the age of the donor at time of death, Dx lists whether the donor was diagnosed as schizophrenic or was a neurotypical control, Sex and Race list these demographic characteristics for each sample, pH lists the pH of the brain at collection, PMI is the postmortem interval between death and brain harvesting, BrNum is the donor number, RIN is the RNA Integrity Number for the RNA sample, LibraryProtocol categorizes the RNAseq library preparation method as polyA selection ("polyA") or rRNA depletion ("Ribo"), SampleID is the ID for the sample, totalAssignedGene is the proportion of reads mapping to a gene body, sumMapped is the number of mapped reads, BigWig is the name of the BigWig file, SampleID_library is the Sample ID and library column values together, and files lists the URL for the BigWig online.

Cell

phenotype information for samples from https://www.pnas.org/content/112/23/7285; a data.frame with 466 rows and 11 columns. Column descriptions: geo_accession is the accession number for each sample in the Gene Expression Omnibus, Age is the numeric age of each sample, AgeGroup categorizes each sample age as "prenatal" or "postnatal", sub_tissue lists whether the sample was from cortex or hippocampus, Cluster_color is the color for each sample for plotting, Cell_type is the cell identity assigned to each sample, RunName is the run name assigned to each sample in the Sequence Read Archive (SRA), SubjectID is the subject label, sumMapped is the number of mapped reads, BigWig is the name of the BigWig file, and files lists the URL for the BigWig online.

Sort

phenotype information for samples from https://www.biorxiv.org/content/10.1101/428391v2; a data.frame with 12 rows and 12 columns. Column descriptions: Description categorizes the RNAseq library preparation method as polyA selection ("PolyA") or rRNA depletion ("Ribo"), SubjectID is the subject number, CellType lists whether the sample was labeled by NeuN antibody (neuronal, "NeuN_Plus") or not (non-neuronal, "NeuN_Minus"), SampleID combines the sample number, cell type and library of each sample in one column, BrNum is the donor ID, RIN is the RNA Integrity Number for each RNA sample, Age is the numeric age at death, sumMapped is the number of mapped reads, Label and col provide information for plotting, BigWig is the name of each BigWig file, and files lists the URL for the BigWig online.

See Also

four_panels brainflowprobes_cov https://github.com/LieberInstitute/brainflowprobes/blob/devel/data-raw/create_sysdata.R

Examples

##  pd <- list(Sep = pdSep, Deg = pdDeg, Cell = pdCell, Sort = pdSort)

LieberInstitute/brainflowprobes documentation built on Dec. 13, 2024, 11:19 p.m.