synlet (version 1.2.2)

rsaHits: Select hits by RSA

Description

Selected hits by redundant siRNA activity method. Here is a wrapper function of RSA 1.8 by Yingyao Zhou.

Usage

rsaHits(dat, treatment, control, normMethod = "PLATE", LB, UB,
  revHits = FALSE, Bonferroni = FALSE, outputFile = "RSAhits.csv",
  scoreFile = "RSA_score.csv")

Arguments

dat

synthetic lethal RNAi screen data

treatment

the treatment condition in EXPERIMENT_MODIFICATION

control

the control condition in EXPERIMENT_MODIFICATION

normMethod

normalization methods. If "PLATE", then values are normalized by plate median, otherwise use the provided control siRNA

LB

Low bound

UB

up bound

revHits

reverse hit picking, default the lower the score the better

Bonferroni

conceptually useful when there are different number of siRNAs per gene, default FALSE

outputFile

output file name

scoreFile

name of the score file to be written under the current folder

Value

• A result file written to the current folder.
  • Gene_ID,Well_ID,Score: columns from input spreadsheet
  • LogP: OPI p-value in log10, i.e., -2 means 0.01
  • OPI_Hit: whether the well is a hit, 1 means yes, 0 means no
  • #hitWell: number of hit wells for the gene
  • #totalWell: total number of wells for the gene. If gene A has three wells w1, w2 and w3, and w1 and w2 are hits, #totalWell should be 3, #hitWell should be 2, w1 and w2 should have OPI_Hit set as 1 and w3 should have OPI_Hit set as 0.
  • OPI_Rank: ranking column to sort all wells for hit picking
  • Cutoff_Rank: ranking column to sort all wells based on Score in the simple activity-based method
  Note: a rank value of 999999 means the well is not a hit

References

Koenig, R. et al. A probability-based approach for the analysis of large-scale RNAi screens. Nat Methods 4, 847-849 (2007).

Examples

rsaHits(exampleDat, treatment = "treatment", control = "control",
  normMethod = "PLATE", LB = 0.2, UB = 0.8, revHits = FALSE,
  Bonferroni = FALSE, outputFile = "RSAhits.csv")