HT.29correctedFCs: CRISPRcleanR corrected data for an example cell line

In francescojm/CRISPRcleanR: Unsupervised correction of gene independent cell responses to CRISPR-cas9 targeting

CRISPRcleanR corrected data for an example cell line

Description

This list contains corrected sgRNAs log fold-changes and segment annotations for an example cell line (HT-29), obtained using the ccr.GWclean function, as detailed in its reference manual entry ccr.GWclean.

Usage

data("HT.29correctedFCs")

Format

A list containing two data frames and a vector of strings. The first data frame (corrected_logFCs) contains a named row per each sgRNA and the following columns/header:

• CHR: the chromosome of the gene targeted by the sgRNA under consideration;

• startp: the genomic coordinate of the starting position of the region targeted by the sgRNA under consideration;

• endp: the genomic coordinate of the ending position of the region targeted by the sgRNA under consideration;

• genes: the HGNC symbol of the gene targeted by the sgRNA under consideration;

• avgFC: the log fold change of the sgRNA averaged across replicates;

• correction: the type of correction: 1 = increased log fold change, -1 = decreased log fold change. 0 indicates no correction;

• correctedFC: the corrected log fold change of the sgRNA

.
The second data frame (segments) contains the identified region of estimated equal log fold changes (one region per row) and the following columns/headers:

• CHR: the chromosome of the gene targeted by the sgRNA under consideration;

• startp: the genomic coordinate of the starting position of the region targeted by the sgRNA under consideration;

• endp: the genomic coordinate of the ending position of the region targeted by the sgRNA under consideration;

• genes: the HGNC symbol of the gene targeted by the sgRNA under consideration;

• avgFC: the log fold change of the sgRNA averaged across replicates;

• correction: the type of correction: 1 = increased log fold change, -1 = decreased log fold change. 0 indicates no correction;

• correctedFC: the corrected log fold change of the sgRNA

.
The second data frame (segments) contains the identified region of estimated equal log fold changes (one region per row) and the following columns/headers:

• CHR: the chromosome of the region under consideration;

• startp: the genomic coordinate of the starting position of the region under consideration;

• endp: the genomic coordinate of the ending position of the region under consideration;

• n.sgRNAs: the number of sgRNAs targeting sequences in the region under consideration;

• avg.logFC: the average log fold change of the sgRNAs in the region;

• guideIdx: the indexes range of the sgRNAs targeting the region under consideration as they appear in the gwSortedF Cs provided in input.

The string of vectors (SORTED_sgRNAs) contains the sgRNAs' identifiers in the same order as they are reported in the gwSortedFCs data frame inputted to the ccr.GWclean function.

Examples

data(HT.29correctedFCs)
head(HT.29correctedFCs$corrected_logFCs)
head(HT.29correctedFCs$segments)
head(HT.29correctedFCs$SORTED_sgRNAs)

francescojm/CRISPRcleanR documentation built on April 30, 2023, 5:41 a.m.